tabix parse error and cluster-bins failure

[csmoreno]

Consistently getting a tabix parse error
"[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?"

and also getting this error which kills the pipeline at the cluster-bins step:

[0mTraceback (most recent call last):
File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/bin/hatchet", line 8, in
sys.exit(main())
File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/main.py", line 61, in main
globals()command
File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/run.py", line 316, in main
cluster_bins(
File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/cluster_bins.py", line 71, in main
assert str(start_row[0]) == my_chr, (start_row[0], my_chr)
AssertionError: ('chr1', "('chr1',)")

If I try to run the demo-wes.sh script on the example data, I get this error:

java version "19.0.1" 2022-10-18
Java(TM) SE Runtime Environment (build 19.0.1+10-21)
Java HotSpot(TM) 64-Bit Server VM (build 19.0.1+10-21, mixed mode, sharing)

• PS4='[\t]'
  [10:01:33]:
  [10:01:33]python3 -m hatchet cluster-bins demo-wes.bb -o demo-wes.seg -O demo-wes.bbc -d 0.08
  �[1m�[95m[2023-Jun-01 10:01:38]# Parsing and checking input arguments
  �[0m�[92m
  bbfile: demo-wes.bb
  diploidbaf: 0.08
  decoding: map
  minK: 2
  maxK: 30
  exactK: 0
  covar: diag
  transmat: diag
  tau: 1e-06
  outsegments: demo-wes.seg
  outbins: demo-wes.bbc
  restarts: 10
  subset: None
  �[0m�[1m�[95m[2023-Jun-01 10:01:38]# Reading the combined BB file
  �[0mTraceback (most recent call last):
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/runpy.py", line 197, in _run_module_as_main
  return _run_code(code, main_globals, None,
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/runpy.py", line 87, in _run_code
  exec(code, run_globals)
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/main.py", line 65, in
  sys.exit(main())
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/main.py", line 61, in main
  globals()command
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/cluster_bins.py", line 21, in main
  tracks, bb, sample_labels, chr_labels = read_bb(args['bbfile'], subset=args['subset'])
  File "/opt/scratchspace/cmoreno/anaconda3/envs/hatchet/lib/python3.9/site-packages/hatchet/utils/cluster_bins.py", line 158, in read_bb
  assert len(gaps) == 1, 'Found a chromosome with >1 gaps between bins'
  AssertionError: Found a chromosome with >1 gaps between bins

Any help is much appreciated. Thanks

[ronkesm]

Were you able to troubleshoot this? I can circumvent the error by using the (deprecated?) cluster-bins-gmm but then it fails on the compute-cn step instead (Raised here #193 ). I also get the tabix error preceding this.

[tmfreeman400]

Were either of you able to solve the error in cluster-bins in the end? If so, did you determine what the cause was? I am also getting the same error:
assert str(start_row[0]) == my_chr, (start_row[0], my_chr) AssertionError: ('chr1', "('chr1',)")

I also had text in cluster-bins error log indicating that the model was not converging, in case this is related:
"Model is not converging. Current: 21469.297836887617 is not greater than 21469.305961301663. Delta is -0.008124414045596495"

Any help would be greatly appreciated.

[csmoreno]

I had a real challenge working through this. What I ended up doing was running the first half of the analysis with version 1.2.1 until I get this error, and then taking the output files from the point of this error and running them through the rest of the pipeline using version 1.1.1. I did have to reformat the bulk.bb files to have the correct columns and order of chromosomes. However, they have now released version 2.0.1, so hopefully the issue has been resolved. From: Tim Freeman ***@***.***> Date: Thursday, December 21, 2023 at 6:31 PM To: raphael-group/hatchet ***@***.***> Cc: Moreno, Carlos S ***@***.***>, Author ***@***.***> Subject: [External] Re: [raphael-group/hatchet] tabix parse error and cluster-bins failure (Issue #188) Were either of you able to solve the error in cluster-bins in the end? If so, did you determine what the cause was? I am also getting the same error: assert str(start_row[0]) == my_chr, (start_row[0], my_chr) AssertionError: ('chr1', "('chr1',)") I also had text in cluster-bins error log indicating that the model was not converging, in case this is related: "Model is not converging. Current: 21469.297836887617 is not greater than 21469.305961301663. Delta is -0.008124414045596495" Any help would be greatly appreciated. — Reply to this email directly, view it on GitHub<#188 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACQBIXCQU2DAS4FKVKCDVZLYKTBFJAVCNFSM6AAAAAAYVSA6JOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRXGA2TAMZUGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[tmfreeman400]

Thank you very much for your fast response csmoreno! The issue has indeed been resolved with the new version (2.0.1) and the error isn't happening anymore. :)