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I was running the pipeline for the FoldTree with my custom dataset of pdbs. And it keeps crashing.
This is the message/output from the .log file. Can you help me understand why this is happening?
Config file /mnt/researchdrive/Kaustubh/RbcS_Origin/data/Structures/Colabfold_Phylogeny_Seqs/FoldTree_Phylogeny/fold_tree/workflow/config/config_vars.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Relative file path './results/plddt.json' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/plddt.json' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/plddt.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/sequence_dataset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/sequences.fst' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/dlstructs.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/identifiers.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/sequence_dataset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/dlsequences.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/allvall_1.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/foldtree_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldseek2distmat.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/finalset.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/allvall_1.csv' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldseekallvall.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/alntmscore_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.PP.nwk.rooted.final' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.PP.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_fastmemat.txt' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/lddt_struct_tree.nwk' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/plddt.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/dlstructs.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/dlsequences.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldtree_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldseek2distmat.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/foldseekallvall.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/alntmscore_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_struct_madroot_post.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_struct_postprocess.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Relative file path './results/logs/lddt_quicktree.log' starts with './'. This is redundant and strongly discouraged. It can also lead to inconsistent results of the file-matching approach used by Snakemake. You can simply omit the './' for relative file paths.
Using shell: /usr/bin/bash
Provided cores: 12
Rules claiming more threads will be scaled down.
Job stats:
job count
------------------ -------
all 1
dl_ids_sequences 1
dl_ids_structs 1
foldseek2distmat 1
foldseek_allvall_1 1
mad_root_post 3
plddt 1
postprocess 3
quicktree 3
total 15
Select jobs to execute...
[Tue Feb 27 18:00:39 2024]
rule dl_ids_sequences:
input: ./results/identifiers.txt
output: ./results/sequence_dataset.csv
log: ./results/logs/dlsequences.log
jobid: 3
reason: Missing output files: ./results/sequence_dataset.csv
wildcards: folder=./results
resources: tmpdir=/tmp
Activating conda environment: foldtree
Activating conda environment: foldtree
[Tue Feb 27 18:00:42 2024]
Finished job 3.
1 of 15 steps (7%) done
Select jobs to execute...
[Tue Feb 27 18:00:42 2024]
rule dl_ids_structs:
input: ./results/sequence_dataset.csv
output: ./results/sequences.fst, ./results/finalset.csv
log: ./results/logs/dlstructs.log
jobid: 2
reason: Missing output files: ./results/finalset.csv; Input files updated by another job: ./results/sequence_dataset.csv
wildcards: folder=./results
resources: tmpdir=/tmp
Activating conda environment: foldtree
Activating conda environment: foldtree
[Tue Feb 27 18:00:43 2024]
Finished job 2.
2 of 15 steps (13%) done
Select jobs to execute...
[Tue Feb 27 18:00:43 2024]
rule plddt:
input: ./results/finalset.csv
output: ./results/plddt.json
log: ./results/logs/plddt.log
jobid: 1
reason: Missing output files: ./results/plddt.json; Input files updated by another job: ./results/finalset.csv
wildcards: folder=./results
resources: tmpdir=/tmp
[Tue Feb 27 18:00:43 2024]
rule foldseek_allvall_1:
input: ./results/finalset.csv
output: ./results/allvall_1.csv
log: ./results/logs/foldseekallvall.log
jobid: 8
reason: Missing output files: ./results/allvall_1.csv; Input files updated by another job: ./results/finalset.csv
wildcards: folder=./results
resources: tmpdir=/tmp
Activating conda environment: foldtree
Activating conda environment: foldtree
Activating conda environment: foldtree
[Tue Feb 27 18:00:43 2024]
Error in rule foldseek_allvall_1:
jobid: 8
input: ./results/finalset.csv
output: ./results/allvall_1.csv
log: ./results/logs/foldseekallvall.log (check log file(s) for error details)
conda-env: foldtree
shell:
foldseek easy-search ./results/structs/ ./results/structs/ ./results/allvall_1.csv ./results/tmp --format-output 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore' --exhaustive-search --alignment-type 2 -e inf --threads 1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Tue Feb 27 18:01:00 2024]
Finished job 1.
3 of 15 steps (20%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-02-27T180039.114096.snakemake.log
I also tried it on Google collab and this is the error I get:
If I had to venture a guess it looks like foldseek is throwing an error in both cases. We had seen this during the all vs all comparison with some previous versions. Make sure the structs folder contains valid PDB files. If it still doesn't work, I would try to run a foldseek all vs all command on the command line outside of snakemake using the foldseek conda environment. This may be more of a problem to report to the foldseek git. Since I wasn't involved in the development of that tool I really can't be of much more use. Sorry.
Hey @kaustubh-amritkar, were you able to resolve it? I have the same issue, while running foldtree colab on the same set of pdb files that were analyzed successfully just last week
I was running the pipeline for the FoldTree with my custom dataset of pdbs. And it keeps crashing.
This is the message/output from the .log file. Can you help me understand why this is happening?
I also tried it on Google collab and this is the error I get:
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