diff --git a/orthohmm/externals.py b/orthohmm/externals.py index 100e689..f4ccdc2 100644 --- a/orthohmm/externals.py +++ b/orthohmm/externals.py @@ -1,7 +1,9 @@ +import math import multiprocessing from multiprocessing.synchronize import Lock from multiprocessing.sharedctypes import Synchronized import subprocess +import sys from typing import List @@ -21,11 +23,12 @@ def update_progress( lock: Lock, completed_tasks: Synchronized, total_tasks: int, -) -> None: +) -> None: with lock: completed_tasks.value += 1 progress = (completed_tasks.value / total_tasks) * 100 - print(f" {progress:.1f}% complete") + sys.stdout.write(f"\r {math.floor(progress)}% complete") + sys.stdout.flush() def execute_phmmer_search( @@ -37,7 +40,7 @@ def execute_phmmer_search( pool = multiprocessing.Pool(processes=cpu) # Create a counter and lock for tracking progress - completed_tasks = multiprocessing.Value('i', 0) + completed_tasks = multiprocessing.Value("i", 0) total_tasks = len(phmmer_cmds) lock = multiprocessing.Lock() diff --git a/orthohmm/orthohmm.py b/orthohmm/orthohmm.py index c764593..42ff239 100644 --- a/orthohmm/orthohmm.py +++ b/orthohmm/orthohmm.py @@ -4,7 +4,7 @@ import os import sys import time -from typing import Union +from typing import Union, List from .args_processing import process_args from .externals import ( @@ -52,7 +52,7 @@ def execute( # get FASTA files to identify orthologs from extensions = (".fa", ".faa", ".fas", ".fasta") - files = [file for file in os.listdir(fasta_directory) if os.path.splitext(file)[1].lower() in extensions] + files: List[str] = [file for file in os.listdir(fasta_directory) if os.path.splitext(file)[1].lower() in extensions] if start != StartStep.search_res: phmmer_cmds = generate_phmmer_cmds( @@ -102,7 +102,7 @@ def execute( phmmer_cmds, cpu, ) - print(" Completed!\n") + print("\r Completed! \n") current_step += 1 print(f"Step {current_step}/{total_steps}: Determining edge thresholds") diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 6d5a8c0..1908bae 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - WBGene00013724.1 - 9.1e-152 489.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index c326faa..a08fb51 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSCAFP00000048558 - WBGene00013724.1 - 4.3e-60 190.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 81c5b5f..f4cdeb6 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSCINP00000010262 - WBGene00013724.1 - 4.1e-65 207.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 39e3632..6713a59 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -10,9 +10,9 @@ ENSDARP00000149121 - WBGene00013724.1 - 4e-50 159.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 09ed2a8..36c0b56 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSGALP00000028084 - WBGene00013724.1 - 1.8e-65 208.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 1b41506..6909596 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSP00000340836 - WBGene00013724.1 - 4.7e-68 216.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 1b8aa84..62a6f3d 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSMODP00000002384 - WBGene00013724.1 - 1.8e-68 218.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 01894c7..a825dc1 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSMUSP00000025631 - WBGene00013724.1 - 3.7e-67 214.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 13cdb21..626f4f9 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSPTRP00000079818 - WBGene00013724.1 - 4.7e-68 216.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index f1eed49..2bff9a7 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - WBGene00013724.1 - 4e-68 217.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index c6a7267..011e1c2 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ ENSTNIP00000019800 - WBGene00013724.1 - 2.2e-65 208.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 14a4ba6..b80c4e8 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSCAFP00000048558 - 1.3e-60 192.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:06 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 170f5ef..e6b0f53 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSCAFP00000017344 - 0 5307.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:04 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 55ad98e..27d809b 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSCAFP00000017344 - 1.3e-291 958.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:06 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index b3472c4..10a2f3b 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSCAFP00000017344 - 0 3406.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:05 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index e32966f..3213ca5 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSCAFP00000017344 - 0 4126.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:06 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index dc514a9..33baf3d 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSCAFP00000017344 - 0 4968.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:05 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index c07cd5e..fd7f1bb 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSCAFP00000017344 - 0 4656.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:06 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index e40ca7f..1043510 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSCAFP00000017344 - 0 4829.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:04 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 1860893..6c21b7b 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSCAFP00000017344 - 0 4983.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:05 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 2d7c4b4..b660e6f 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSCAFP00000048558 - 1.4e-125 407.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:06 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index c0bc32a..a7cc70b 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSCAFP00000017344 - 0 3325.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:05 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index baa422f..bf268f7 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSCINP00000010262 - 2.5e-65 207.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index ae24957..045bf29 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSCINP00000024362 - 1.5e-292 961.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index d49ff1d..274903b 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSCINP00000024362 - 0 3552.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 1a81e7b..3eed190 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSCINP00000024362 - 1.3e-283 932.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 5c4c9e4..569846d 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSCINP00000024362 - 1.3e-293 964.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index ac453a2..1ea2d8e 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSCINP00000024362 - 2.3e-288 947.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 8284989..db84223 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSCINP00000024362 - 3.7e-297 976.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:21 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 8077125..096c6f8 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSCINP00000024362 - 5.2e-290 953.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 2036bbd..445e36c 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSCINP00000024362 - 4.7e-288 946.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 78d2a08..c67e893 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSCINP00000010262 - 4.5e-74 236.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:20 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 98f19d5..9dc4c18 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSCINP00000024362 - 1.3e-279 918.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Ciona_intestinalis.KH.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index e05533a..b612543 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -10,9 +10,9 @@ WBGene00013724.1 - ENSDARP00000149121 - 2.2e-51 161.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:13 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index bd3ad14..b502aee 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSCAFP00000017344 - ENSDARP00000129655 - 0 3409.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:12 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 988466e..8a7be17 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSCINP00000024362 - ENSDARP00000129655 - 2e-284 934.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:14 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index fdec12c..db24da1 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -19,9 +19,9 @@ ENSDARP00000129655 - ENSDARP00000129655 - 0 5322.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:13 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 6f61d33..5867f2a 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSGALP00000046461 - ENSDARP00000129655 - 0 3423.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:14 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 16a574f..370b623 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSP00000260197 - ENSDARP00000129655 - 0 3439.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:13 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 443a750..0d2a9ad 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSMODP00000016287 - ENSDARP00000129655 - 0 3474.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:15 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 30dfcb3..4b79460 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSMUSP00000058613 - ENSDARP00000129655 - 0 3430.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:12 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 85786e5..9eee36f 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSPTRP00000007532 - ENSDARP00000129655 - 0 3439.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:13 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index de367f2..c3f99ff 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -13,9 +13,9 @@ ENSRNOP00000016871 - ENSDARP00000149121 - 6.6e-104 333.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:14 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index e632154..89bf4d3 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSTNIP00000017394 - ENSDARP00000129655 - 0 4009.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Danio_rerio.GRCz11.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:12 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 71906ca..723b821 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSGALP00000028084 - 3.7e-66 210.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:22 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 8bcf173..72b2d07 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSGALP00000046461 - 0 4127.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:21 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 0bee8d3..c64ff7e 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSGALP00000046461 - 1.2e-290 954.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:23 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 7800e52..028c88c 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSGALP00000046461 - 0 3421.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:22 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index dda3234..5064da0 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSGALP00000046461 - 0 5310.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:23 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 868a74c..322405d 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSGALP00000046461 - 0 4163.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:22 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 417bdc9..4af6405 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSGALP00000046461 - 0 4256.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:23 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 68793a4..f1c0f7c 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSGALP00000046461 - 0 4101.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:21 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 0688bdc..7f74c39 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSGALP00000046461 - 0 4174.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:22 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index d9b78e7..67bef23 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSGALP00000028084 - 4.1e-141 457.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:23 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index c5aa36d..aff7715 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSGALP00000046461 - 0 3326.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Gallus_gallus.GRCg6a.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:21 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index c6be633..5012632 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSP00000340836 - 1e-68 218.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:16 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 0898755..336d1dd 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSP00000260197 - 0 4969.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:15 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 584abaa..849032d 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSP00000260197 - 2.3e-288 947.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 2ab4d79..abca3a5 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSP00000260197 - 0 3436.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:16 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index c25e910..ea669a7 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSP00000260197 - 0 4163.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 6935bd3..f3ac381 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSP00000260197 - 0 5330.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:16 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 1918f65..7bb2933 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSP00000260197 - 0 4737.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:17 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 470c93a..657abd8 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSP00000260197 - 0 4997.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:15 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index fbc8a34..1f60da4 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSP00000260197 - 0 5306.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:16 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 93b62b9..7fb76aa 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSP00000340836 - 1.1e-145 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:16 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index ef883af..ad26944 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSP00000260197 - 0 3327.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Homo_sapiens.GRCh38.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:15 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index a8fc08b..5e6250d 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSMODP00000002384 - 5.2e-69 219.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:25 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 0699bb6..546c05f 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSMODP00000016287 - 0 4656.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:24 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 91f41dc..c2f9e4c 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSMODP00000016287 - 1.3e-288 947.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:25 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 1f8c4ea..7ed5117 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSMODP00000016287 - 0 3471.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:25 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 839c9e5..81eec7d 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSMODP00000016287 - 0 4255.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:26 2024 +# Date: Mon Aug 26 16:30:25 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index a421152..dfd1d88 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSMODP00000016287 - 0 4737.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:25 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 22f0880..74c88fa 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSMODP00000016287 - 0 5338.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:26 2024 +# Date: Mon Aug 26 16:30:25 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 98520ac..274644c 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSMODP00000016287 - 0 4649.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:24 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 88940ba..35b43b7 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSMODP00000016287 - 0 4745.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:24 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index e99315e..1747037 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSMODP00000002384 - 3.7e-145 468.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:25 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 267a696..883bcdb 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSMODP00000016287 - 0 3367.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:24 2024 +# Date: Mon Aug 26 16:30:24 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 614427c..1ccbff1 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSMUSP00000025631 - 4.9e-68 215.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:03 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 2af769e..eb6828d 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSMUSP00000058613 - 0 4829.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:01 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index a89c914..dc86dcd 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSMUSP00000058613 - 9.1e-293 961.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:03 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 03a8572..8641d91 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSMUSP00000058613 - 0 3427.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:02 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 1ea1b84..27dec55 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSMUSP00000058613 - 0 4100.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:04 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index d1f17af..869a844 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSMUSP00000058613 - 0 4997.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:02 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 2cbe954..f58a671 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSMUSP00000058613 - 0 4649.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:04 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index dce9bc9..58446ff 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -12,9 +12,9 @@ ENSMUSP00000058613 - ENSMUSP00000058613 - 0 5320.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:01 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 0115fe8..785395d 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSMUSP00000058613 - 0 5013.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:02 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index fc2d8e1..416b8a7 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,9 +10,9 @@ ENSRNOP00000065522 - ENSMUSP00000086314 - 7.7e-256 838.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:03 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 8f2d70c..3be8ca7 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSMUSP00000058613 - 0 3345.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Mus_musculus.GRCm38.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:02 2024 +# Date: Mon Aug 26 16:30:20 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 528db71..4eedacf 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSPTRP00000079818 - 1e-68 218.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:11 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 7b93ae7..667fb60 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSPTRP00000007532 - 0 4983.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:09 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 579ade6..90cce29 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSPTRP00000007532 - 2.7e-288 947.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:11 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 906279c..bfa3495 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSPTRP00000007532 - 0 3436.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:10 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 550b26d..d310395 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSPTRP00000007532 - 0 4173.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:11 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index eb82964..87dd0f9 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSPTRP00000007532 - 0 5306.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:10 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index f9be964..34327ec 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSPTRP00000007532 - 0 4745.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:11 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index e03deee..4d83dd3 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSPTRP00000007532 - 0 5013.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:09 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 567d706..78a8246 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSPTRP00000007532 - 0 5329.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:10 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 0f58700..9632bf0 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSPTRP00000079818 - 1.1e-145 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:11 2024 +# Date: Mon Aug 26 16:30:22 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 0ed1ff3..548a166 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSPTRP00000007532 - 0 3331.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:10 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 9e8a867..5385d9e 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ WBGene00013724.1 - ENSRNOP00000016871 - 6.5e-69 218.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 62da092..2695233 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000048558 - ENSRNOP00000016871 - 2.7e-126 406.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 81707b9..92248fb 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000010262 - ENSRNOP00000016871 - 1.6e-74 237.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index b481aa7..07a985b 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,9 +13,9 @@ ENSDARP00000149121 - ENSRNOP00000016871 - 1.9e-103 333.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 07fdee7..267fed8 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000028084 - ENSRNOP00000016871 - 9.8e-142 457.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index a46bc0a..e512aab 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000340836 - ENSRNOP00000016871 - 8e-146 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 500888f..495e1e8 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000002384 - ENSRNOP00000016871 - 2.3e-145 469.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:19 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 8087df7..6c1f419 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,9 +10,9 @@ ENSMUSP00000086311 - ENSRNOP00000065522 - 1.9e-255 836.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 9aa2c40..c056d79 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000079818 - ENSRNOP00000016871 - 8e-146 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index a8d5bf5..2b13840 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSRNOP00000065522 - ENSRNOP00000065522 - 0 1213.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index c681a65..7ccff43 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000019800 - ENSRNOP00000016871 - 3.1e-130 419.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:18 2024 +# Date: Mon Aug 26 16:30:23 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 77ab280..83b7fd8 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSTNIP00000019800 - 6.1e-66 209.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:08 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 5816e3b..f03b3f3 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSTNIP00000017394 - 0 3329.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:07 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 00c1846..75add1d 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSTNIP00000017394 - 4.9e-284 933.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:08 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 3e3b933..ac2eaac 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSTNIP00000017394 - 0 4011.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:08 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index e732961..1bee9b3 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSTNIP00000017394 - 0 3328.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:09 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 55635d3..89fec19 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSP00000260197 - ENSTNIP00000017394 - 0 3332.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:08 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 0836d23..4657c23 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSTNIP00000017394 - 0 3370.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:09 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 58913e9..e39c347 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSTNIP00000017394 - 0 3349.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:07 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 11004b0..1c58e84 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSTNIP00000017394 - 0 3336.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:07 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 0aca06e..8f167b0 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSTNIP00000019800 - 5e-130 419.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:08 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 8e2eeae..812ef45 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSTNIP00000017394 - 0 5341.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # Pipeline mode: SEARCH -# Query file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Mon Aug 26 08:38:07 2024 +# Date: Mon Aug 26 16:30:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/orthohmm_edges.txt b/tests/samples/orthohmm_working_res/orthohmm_edges.txt index 1af971d..a273a25 100644 --- a/tests/samples/orthohmm_working_res/orthohmm_edges.txt +++ b/tests/samples/orthohmm_working_res/orthohmm_edges.txt @@ -1,181 +1,181 @@ ENSMUSP00000086311 ENSMUSP00000086314 0.9452235456218643 -ENSMUSP00000032440 ENSCAFP00000053904 1.1765339326216484 -ENSMUSP00000058613 ENSCAFP00000017344 1.1191809742240841 +ENSCAFP00000053904 ENSMUSP00000032440 1.1765339326216484 +ENSCAFP00000017344 ENSMUSP00000058613 1.1191809742240841 ENSTNIP00000005325 ENSMUSP00000032440 1.1230455740952423 -ENSMUSP00000025631 ENSTNIP00000019800 1.0573543116888735 +ENSTNIP00000019800 ENSMUSP00000025631 1.0573543116888735 ENSMUSP00000058613 ENSTNIP00000017394 0.8204945552781063 -ENSMUSP00000032440 ENSPTRP00000071151 0.9750143971399228 -ENSMUSP00000025631 ENSPTRP00000079818 0.9947457998525575 -ENSMUSP00000058613 ENSPTRP00000007532 1.0305438528225042 +ENSPTRP00000071151 ENSMUSP00000032440 0.9750143971399228 +ENSPTRP00000079818 ENSMUSP00000025631 0.9947457998525575 +ENSPTRP00000007532 ENSMUSP00000058613 1.0305438528225042 ENSDARP00000071531 ENSMUSP00000032440 1.1405390347688653 -ENSMUSP00000032440 ENSDARP00000147265 1.109983290000416 -ENSMUSP00000032440 ENSDARP00000154605 1.1083231295307774 -ENSMUSP00000025631 ENSDARP00000110254 1.014393194490703 -ENSMUSP00000025631 ENSDARP00000149121 0.8935016279742156 +ENSDARP00000147265 ENSMUSP00000032440 1.109983290000416 +ENSDARP00000154605 ENSMUSP00000032440 1.1083231295307774 +ENSDARP00000110254 ENSMUSP00000025631 1.014393194490703 +ENSDARP00000149121 ENSMUSP00000025631 0.8935016279742156 ENSMUSP00000058613 ENSDARP00000129655 0.8464014718555611 -ENSMUSP00000032440 ENSP00000373312 0.9739080572466866 -ENSMUSP00000025631 ENSP00000340836 0.996854926953224 +ENSP00000373312 ENSMUSP00000032440 0.9739080572466866 +ENSP00000340836 ENSMUSP00000025631 0.996854926953224 ENSMUSP00000058613 ENSP00000260197 1.029618128104977 -ENSMUSP00000032440 WBGene00003806.1 0.9330346205728083 -ENSMUSP00000025631 WBGene00013724.1 1.078616751331466 -ENSMUSP00000032440 ENSRNOP00000014377 1.1575744132634167 -ENSMUSP00000025631 ENSRNOP00000016871 1.118452164541046 +WBGene00003806.1 ENSMUSP00000032440 0.9330346205728083 +WBGene00013724.1 ENSMUSP00000025631 1.078616751331466 +ENSRNOP00000014377 ENSMUSP00000032440 1.1575744132634167 +ENSRNOP00000016871 ENSMUSP00000025631 1.118452164541046 ENSRNOP00000065522 ENSMUSP00000086314 0.724492027798829 ENSMUSP00000032440 ENSCINP00000005198 1.524489076894231 -ENSMUSP00000025631 ENSCINP00000010262 0.998945905307546 -ENSMUSP00000058613 ENSCINP00000024362 0.4807572315142691 -ENSMUSP00000025631 ENSGALP00000028084 0.981655351115904 -ENSMUSP00000058613 ENSGALP00000046461 1.0971675453571852 -ENSMUSP00000032440 ENSMODP00000006811 1.035122951917207 -ENSMUSP00000025631 ENSMODP00000002384 1.001174747698835 +ENSCINP00000010262 ENSMUSP00000025631 0.998945905307546 +ENSCINP00000024362 ENSMUSP00000058613 0.4807572315142691 +ENSGALP00000028084 ENSMUSP00000025631 0.981655351115904 +ENSGALP00000046461 ENSMUSP00000058613 1.0971675453571852 +ENSMODP00000006811 ENSMUSP00000032440 1.035122951917207 +ENSMODP00000002384 ENSMUSP00000025631 1.001174747698835 ENSMUSP00000058613 ENSMODP00000016287 0.9642127408498951 -ENSMUSP00000025631 ENSCAFP00000048558 0.7048020506658835 +ENSCAFP00000048558 ENSMUSP00000025631 0.7048020506658835 ENSTNIP00000005325 ENSCAFP00000053904 1.29041322599113 -ENSTNIP00000019800 ENSCAFP00000048558 0.773726752517809 -ENSTNIP00000017394 ENSCAFP00000017344 0.9375675734980686 +ENSCAFP00000048558 ENSTNIP00000019800 0.773726752517809 +ENSCAFP00000017344 ENSTNIP00000017394 0.9375675734980686 ENSCAFP00000053904 ENSPTRP00000071151 1.1117442428910387 -ENSPTRP00000079818 ENSCAFP00000048558 0.7222433706443235 +ENSCAFP00000048558 ENSPTRP00000079818 0.7222433706443235 ENSCAFP00000017344 ENSPTRP00000007532 1.1666255159560786 ENSCAFP00000053904 ENSDARP00000147265 1.2662879716451452 ENSCAFP00000053904 ENSDARP00000154605 1.264976532704249 -ENSDARP00000071531 ENSCAFP00000053904 1.2961637997082234 -ENSDARP00000110254 ENSCAFP00000048558 0.7495847510861663 +ENSCAFP00000053904 ENSDARP00000071531 1.2961637997082234 +ENSCAFP00000048558 ENSDARP00000110254 0.7495847510861663 ENSCAFP00000017344 ENSDARP00000129655 0.9559051251977784 -ENSCAFP00000053904 ENSP00000373312 1.110881900680476 -ENSP00000340836 ENSCAFP00000048558 0.7239183668098337 +ENSP00000373312 ENSCAFP00000053904 1.110881900680476 +ENSCAFP00000048558 ENSP00000340836 0.7239183668098337 ENSCAFP00000017344 ENSP00000260197 1.1659756100193193 ENSCAFP00000053904 WBGene00003806.1 1.1458763815202004 -WBGene00013724.1 ENSCAFP00000048558 0.8693032690258004 -ENSCAFP00000053904 ENSRNOP00000014377 1.2497712083745642 -ENSRNOP00000016871 ENSCAFP00000048558 0.750765381543786 +ENSCAFP00000048558 WBGene00013724.1 0.8693032690258004 +ENSRNOP00000014377 ENSCAFP00000053904 1.2497712083745642 +ENSCAFP00000048558 ENSRNOP00000016871 0.750765381543786 ENSCAFP00000053904 ENSCINP00000005198 1.6887514905455063 -ENSCINP00000010262 ENSCAFP00000048558 0.7763303207340811 +ENSCAFP00000048558 ENSCINP00000010262 0.7763303207340811 ENSCAFP00000053904 ENSGALP00000060372 1.032440253327753 -ENSGALP00000028084 ENSCAFP00000048558 0.7319060730167674 -ENSCAFP00000017344 ENSGALP00000046461 1.2366809018588243 -ENSCAFP00000053904 ENSMODP00000006811 1.1768064885005973 -ENSMODP00000002384 ENSCAFP00000048558 0.7250057434303576 -ENSMODP00000016287 ENSCAFP00000017344 1.0991546578371612 +ENSCAFP00000048558 ENSGALP00000028084 0.7319060730167674 +ENSGALP00000046461 ENSCAFP00000017344 1.2366809018588243 +ENSMODP00000006811 ENSCAFP00000053904 1.1768064885005973 +ENSCAFP00000048558 ENSMODP00000002384 0.7250057434303576 +ENSCAFP00000017344 ENSMODP00000016287 1.0991546578371612 ENSTNIP00000005325 ENSPTRP00000071151 1.078068617227524 -ENSTNIP00000019800 ENSPTRP00000079818 1.0816122924235794 -ENSTNIP00000017394 ENSPTRP00000007532 0.8411232457073231 +ENSPTRP00000079818 ENSTNIP00000019800 1.0816122924235794 +ENSPTRP00000007532 ENSTNIP00000017394 0.8411232457073231 ENSTNIP00000005325 ENSDARP00000071531 1.1071998554333529 ENSTNIP00000005325 ENSDARP00000147265 1.080236084220364 ENSTNIP00000005325 ENSDARP00000154605 1.0793124107836642 -ENSDARP00000110254 ENSTNIP00000019800 0.9783171648990983 -ENSTNIP00000019800 ENSDARP00000149121 0.8594599323873157 +ENSTNIP00000019800 ENSDARP00000110254 0.9783171648990983 +ENSDARP00000149121 ENSTNIP00000019800 0.8594599323873157 ENSTNIP00000017394 ENSDARP00000129655 0.9153920541003192 ENSTNIP00000005325 ENSP00000373312 1.0760130248575053 ENSTNIP00000019800 ENSP00000340836 1.0832989464755691 ENSTNIP00000017394 ENSP00000260197 0.8413995792976301 ENSTNIP00000005325 WBGene00003806.1 0.9341684397011618 -WBGene00013724.1 ENSTNIP00000019800 1.0783142114156974 +ENSTNIP00000019800 WBGene00013724.1 1.0783142114156974 ENSTNIP00000005325 ENSRNOP00000014377 1.0277296796262056 ENSTNIP00000019800 ENSRNOP00000016871 0.9726176544674653 ENSTNIP00000005325 ENSCINP00000005198 1.5030185275774275 -ENSTNIP00000019800 ENSCINP00000010262 1.0308419087795246 -ENSTNIP00000017394 ENSCINP00000024362 0.4718462562136554 +ENSCINP00000010262 ENSTNIP00000019800 1.0308419087795246 +ENSCINP00000024362 ENSTNIP00000017394 0.4718462562136554 ENSTNIP00000005325 ENSGALP00000060372 0.9808125708283421 ENSGALP00000028084 ENSTNIP00000019800 1.022483154403245 -ENSTNIP00000017394 ENSGALP00000046461 0.998411869291212 +ENSGALP00000046461 ENSTNIP00000017394 0.998411869291212 ENSTNIP00000005325 ENSMODP00000006811 1.1315750573240722 -ENSMODP00000002384 ENSTNIP00000019800 1.0525305957202595 -ENSMODP00000016287 ENSTNIP00000017394 0.816761291983043 -ENSDARP00000071531 ENSPTRP00000071151 1.0948975951481827 -ENSDARP00000147265 ENSPTRP00000071151 1.0690571934317779 -ENSDARP00000154605 ENSPTRP00000071151 1.0688977991879383 -ENSDARP00000110254 ENSPTRP00000079818 1.0342390860229558 -ENSPTRP00000079818 ENSDARP00000149121 0.9106986195805375 -ENSDARP00000129655 ENSPTRP00000007532 0.8719045883246118 +ENSTNIP00000019800 ENSMODP00000002384 1.0525305957202595 +ENSTNIP00000017394 ENSMODP00000016287 0.816761291983043 +ENSPTRP00000071151 ENSDARP00000071531 1.0948975951481827 +ENSPTRP00000071151 ENSDARP00000147265 1.0690571934317779 +ENSPTRP00000071151 ENSDARP00000154605 1.0688977991879383 +ENSPTRP00000079818 ENSDARP00000110254 1.0342390860229558 +ENSDARP00000149121 ENSPTRP00000079818 0.9106986195805375 +ENSPTRP00000007532 ENSDARP00000129655 0.8719045883246118 ENSP00000373312 ENSPTRP00000071151 0.9949301160533697 ENSPTRP00000079818 ENSP00000340836 0.979518244878341 -ENSP00000260197 ENSPTRP00000007532 1.0256097745197357 -WBGene00003806.1 ENSPTRP00000071151 0.8995437289862245 -WBGene00013724.1 ENSPTRP00000079818 1.1128612504715538 +ENSPTRP00000007532 ENSP00000260197 1.0256097745197357 +ENSPTRP00000071151 WBGene00003806.1 0.8995437289862245 +ENSPTRP00000079818 WBGene00013724.1 1.1128612504715538 ENSRNOP00000014377 ENSPTRP00000071151 0.9876707502252766 ENSPTRP00000079818 ENSRNOP00000016871 1.0124627007611073 -ENSCINP00000005198 ENSPTRP00000071151 1.4619889679838727 -ENSPTRP00000079818 ENSCINP00000010262 1.0476340139447413 +ENSPTRP00000071151 ENSCINP00000005198 1.4619889679838727 +ENSCINP00000010262 ENSPTRP00000079818 1.0476340139447413 ENSCINP00000024362 ENSPTRP00000007532 0.4933020456912314 -ENSGALP00000060372 ENSPTRP00000071151 0.8900349329976032 -ENSGALP00000028084 ENSPTRP00000079818 0.9800259324955464 +ENSPTRP00000071151 ENSGALP00000060372 0.8900349329976032 +ENSPTRP00000079818 ENSGALP00000028084 0.9800259324955464 ENSGALP00000046461 ENSPTRP00000007532 1.13079100088383 ENSMODP00000006811 ENSPTRP00000071151 0.9749376024616611 -ENSMODP00000002384 ENSPTRP00000079818 1.0286917397835451 -ENSMODP00000016287 ENSPTRP00000007532 0.9969408410146324 +ENSPTRP00000079818 ENSMODP00000002384 1.0286917397835451 +ENSPTRP00000007532 ENSMODP00000016287 0.9969408410146324 ENSDARP00000071531 ENSDARP00000147265 0.9724530402585306 -ENSDARP00000071531 ENSDARP00000154605 0.9724530402585306 +ENSDARP00000154605 ENSDARP00000071531 0.9724530402585306 ENSDARP00000154605 ENSDARP00000147265 1.0056169849533259 -ENSDARP00000110254 ENSDARP00000149121 0.8209655168956405 -ENSDARP00000071531 ENSP00000373312 1.092309927325126 +ENSDARP00000149121 ENSDARP00000110254 0.8209655168956405 +ENSP00000373312 ENSDARP00000071531 1.092309927325126 ENSP00000373312 ENSDARP00000147265 1.0668462539159997 -ENSDARP00000110254 ENSP00000340836 1.03565166616558 -ENSP00000260197 ENSDARP00000129655 0.8729177743346621 -ENSDARP00000071531 WBGene00003806.1 0.9524828140186127 +ENSP00000340836 ENSDARP00000110254 1.03565166616558 +ENSDARP00000129655 ENSP00000260197 0.8729177743346621 +WBGene00003806.1 ENSDARP00000071531 0.9524828140186127 WBGene00013724.1 ENSDARP00000110254 1.061887284814649 -ENSDARP00000071531 ENSRNOP00000014377 1.058713802727288 +ENSRNOP00000014377 ENSDARP00000071531 1.058713802727288 ENSRNOP00000014377 ENSDARP00000147265 1.0302014701833606 ENSDARP00000110254 ENSRNOP00000016871 0.9421452136171529 ENSDARP00000071531 ENSCINP00000005198 1.5381718365133896 -ENSCINP00000005198 ENSDARP00000147265 1.495029099310047 -ENSDARP00000110254 ENSCINP00000010262 0.993006198131263 +ENSDARP00000147265 ENSCINP00000005198 1.495029099310047 +ENSCINP00000010262 ENSDARP00000110254 0.993006198131263 ENSCINP00000024362 ENSDARP00000129655 0.4729883042736134 -ENSDARP00000071531 ENSGALP00000060372 0.994064929295005 +ENSGALP00000060372 ENSDARP00000071531 0.994064929295005 ENSGALP00000028084 ENSDARP00000110254 0.9847113779623486 ENSGALP00000046461 ENSDARP00000129655 1.0222281124094135 -ENSDARP00000071531 ENSMODP00000006811 1.1474514789769603 +ENSMODP00000006811 ENSDARP00000071531 1.1474514789769603 ENSMODP00000006811 ENSDARP00000147265 1.1165699720173847 ENSMODP00000002384 ENSDARP00000110254 1.0133686824287944 -ENSMODP00000016287 ENSDARP00000129655 0.8407101876638388 -ENSDARP00000154605 ENSP00000373312 1.0666866419689747 +ENSDARP00000129655 ENSMODP00000016287 0.8407101876638388 +ENSP00000373312 ENSDARP00000154605 1.0666866419689747 ENSDARP00000149121 ENSP00000340836 0.9119424661952323 -WBGene00003806.1 ENSP00000373312 0.8992587618133254 -WBGene00013724.1 ENSP00000340836 1.1133139966849854 -ENSRNOP00000014377 ENSP00000373312 0.9860799449831307 -ENSRNOP00000016871 ENSP00000340836 1.0141205592757112 -ENSCINP00000005198 ENSP00000373312 1.4611709465315714 +ENSP00000373312 WBGene00003806.1 0.8992587618133254 +ENSP00000340836 WBGene00013724.1 1.1133139966849854 +ENSP00000373312 ENSRNOP00000014377 0.9860799449831307 +ENSP00000340836 ENSRNOP00000016871 1.0141205592757112 +ENSP00000373312 ENSCINP00000005198 1.4611709465315714 ENSCINP00000010262 ENSP00000340836 1.0480563573199848 -ENSGALP00000060372 ENSP00000373312 0.8882376517946002 +ENSP00000373312 ENSGALP00000060372 0.8882376517946002 ENSGALP00000028084 ENSP00000340836 0.9823721009325256 -ENSP00000260197 ENSGALP00000046461 1.1306740611776718 -ENSMODP00000006811 ENSP00000373312 0.9734326265560835 -ENSMODP00000002384 ENSP00000340836 1.0303884611821357 +ENSGALP00000046461 ENSP00000260197 1.1306740611776718 +ENSP00000373312 ENSMODP00000006811 0.9734326265560835 +ENSP00000340836 ENSMODP00000002384 1.0303884611821357 ENSMODP00000016287 ENSP00000260197 0.9968177106624055 WBGene00003806.1 ENSDARP00000147265 0.9035585575356653 WBGene00003806.1 ENSDARP00000154605 0.9035585575356653 -WBGene00013724.1 ENSDARP00000149121 0.8867247529323182 -WBGene00003806.1 ENSRNOP00000014377 0.924003520201405 +ENSDARP00000149121 WBGene00013724.1 0.8867247529323182 +ENSRNOP00000014377 WBGene00003806.1 0.924003520201405 WBGene00013724.1 ENSRNOP00000016871 1.0878197819809396 WBGene00003806.1 ENSCINP00000005198 0.9330541938292204 -WBGene00013724.1 ENSCINP00000010262 1.0742379802460436 +ENSCINP00000010262 WBGene00013724.1 1.0742379802460436 ENSGALP00000028084 WBGene00013724.1 1.1163656112128608 -WBGene00003806.1 ENSMODP00000006811 0.9260965348362314 -ENSMODP00000002384 WBGene00013724.1 1.0848712552404072 -ENSDARP00000154605 ENSRNOP00000014377 1.0286633969224124 -ENSRNOP00000016871 ENSDARP00000149121 0.8303315017735424 -ENSCINP00000005198 ENSRNOP00000014377 1.2020864960788595 +ENSMODP00000006811 WBGene00003806.1 0.9260965348362314 +WBGene00013724.1 ENSMODP00000002384 1.0848712552404072 +ENSRNOP00000014377 ENSDARP00000154605 1.0286633969224124 +ENSDARP00000149121 ENSRNOP00000016871 0.8303315017735424 +ENSRNOP00000014377 ENSCINP00000005198 1.2020864960788595 ENSCINP00000010262 ENSRNOP00000016871 0.7998840304515645 -ENSGALP00000060372 ENSRNOP00000014377 0.9656107168863438 +ENSRNOP00000014377 ENSGALP00000060372 0.9656107168863438 ENSGALP00000028084 ENSRNOP00000016871 1.0358908406122709 -ENSMODP00000006811 ENSRNOP00000014377 1.014568295990869 +ENSRNOP00000014377 ENSMODP00000006811 1.014568295990869 ENSMODP00000002384 ENSRNOP00000016871 0.9858168713252738 -ENSCAFP00000017344 ENSCINP00000024362 0.5392752828930565 +ENSCINP00000024362 ENSCAFP00000017344 0.5392752828930565 ENSDARP00000154605 ENSCINP00000005198 1.491300131871246 ENSCINP00000010262 ENSDARP00000149121 0.8499085703153215 -ENSP00000260197 ENSCINP00000024362 0.4937093636879676 +ENSCINP00000024362 ENSP00000260197 0.4937093636879676 ENSGALP00000060372 ENSCINP00000005198 1.388829513749228 -ENSGALP00000028084 ENSCINP00000010262 1.0053941211274267 +ENSCINP00000010262 ENSGALP00000028084 1.0053941211274267 ENSGALP00000046461 ENSCINP00000024362 0.6139352479277681 ENSMODP00000006811 ENSCINP00000005198 1.512341563219763 -ENSMODP00000002384 ENSCINP00000010262 1.01157228347777 -ENSMODP00000016287 ENSCINP00000024362 0.4844878180487609 -ENSMUSP00000032440 ENSGALP00000060372 0.9226253791108336 -ENSDARP00000147265 ENSGALP00000060372 0.9787006097925798 +ENSCINP00000010262 ENSMODP00000002384 1.01157228347777 +ENSCINP00000024362 ENSMODP00000016287 0.4844878180487609 +ENSGALP00000060372 ENSMUSP00000032440 0.9226253791108336 +ENSGALP00000060372 ENSDARP00000147265 0.9787006097925798 ENSDARP00000154605 ENSGALP00000060372 0.9787006097925798 -ENSGALP00000028084 ENSDARP00000149121 0.8508452087136668 +ENSDARP00000149121 ENSGALP00000028084 0.8508452087136668 WBGene00003806.1 ENSGALP00000060372 0.8967195494012699 ENSMODP00000006811 ENSGALP00000060372 0.9202902491145213 ENSGALP00000028084 ENSMODP00000002384 0.966092055738595 -ENSMODP00000016287 ENSGALP00000046461 1.115319260624795 -ENSDARP00000154605 ENSMODP00000006811 1.115264423964748 -ENSMODP00000002384 ENSDARP00000149121 0.891019663837538 +ENSGALP00000046461 ENSMODP00000016287 1.115319260624795 +ENSMODP00000006811 ENSDARP00000154605 1.115264423964748 +ENSDARP00000149121 ENSMODP00000002384 0.891019663837538 diff --git a/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt b/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt index c4e5425..b12dcd5 100644 --- a/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt +++ b/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt @@ -1,4 +1,4 @@ -ENSMUSP00000032440 ENSCAFP00000053904 ENSTNIP00000005325 ENSPTRP00000071151 ENSDARP00000071531 ENSDARP00000147265 ENSDARP00000154605 ENSP00000373312 WBGene00003806.1 ENSRNOP00000014377 ENSCINP00000005198 ENSMODP00000006811 ENSGALP00000060372 -ENSMUSP00000025631 ENSTNIP00000019800 ENSPTRP00000079818 ENSDARP00000110254 ENSDARP00000149121 ENSP00000340836 WBGene00013724.1 ENSRNOP00000016871 ENSCINP00000010262 ENSGALP00000028084 ENSMODP00000002384 ENSCAFP00000048558 -ENSMUSP00000058613 ENSCAFP00000017344 ENSTNIP00000017394 ENSPTRP00000007532 ENSDARP00000129655 ENSP00000260197 ENSCINP00000024362 ENSGALP00000046461 ENSMODP00000016287 +ENSCAFP00000053904 ENSMUSP00000032440 ENSTNIP00000005325 ENSPTRP00000071151 ENSDARP00000071531 ENSDARP00000147265 ENSDARP00000154605 ENSP00000373312 WBGene00003806.1 ENSRNOP00000014377 ENSCINP00000005198 ENSMODP00000006811 ENSGALP00000060372 +ENSTNIP00000019800 ENSMUSP00000025631 ENSPTRP00000079818 ENSDARP00000110254 ENSDARP00000149121 ENSP00000340836 WBGene00013724.1 ENSRNOP00000016871 ENSCINP00000010262 ENSGALP00000028084 ENSMODP00000002384 ENSCAFP00000048558 +ENSCAFP00000017344 ENSMUSP00000058613 ENSTNIP00000017394 ENSPTRP00000007532 ENSDARP00000129655 ENSP00000260197 ENSCINP00000024362 ENSGALP00000046461 ENSMODP00000016287 ENSMUSP00000086311 ENSMUSP00000086314 ENSRNOP00000065522