IndexError: list index out of range

[Wouter De Coster]

Hi,

I just pulled from GitHub to see if it was already solved, but also the most recent version raises the error below.

This is my command, force calling variants in a bam split by phase

bash <path>/run_clair3.sh --bam_fn=<path>/alignment_HP2.bam --vcf_fn=called_variants.vcf.gz --print_ref_calls --ref_fn=GRCh38.fa --threads=5 --platform="ont" --model_path="<path>/Clair3/models/ont" --output=$output --haploid_sensitive --ctg_name=<chrom> --sample_name=$name

There is a bunch of output before this, and I can email the log files (but not post them here publicly).

== SUMMARY ==
Total alignments processed:                     18712
Alignments that could be tagged:                  641
Alignments spanning multiple phase sets:            0
haplotag - total processing time: 14.516802549362183

real	0m15.604s
user	0m14.753s
sys	0m0.862s

real	0m0.507s
user	0m3.805s
sys	0m0.247s
[INFO] 5/7 Select candidates for full alignment
[INFO] Select variant quality cut off 7.0
[INFO] Select reference quality cut off 21.0
[INFO] Total low qual ref variants to procceed in <chrom>: 11607
[INFO] Total low qual variants to procceed in <chrom>: 261

real	0m0.448s
user	0m0.334s
sys	0m0.134s
[INFO] 6/7 Calling variants using Full Alignment
[INFO] Delay 9 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
  File "/home/wdecoster/repositories/Clair3/clair3/../clair3.py", line 89, in <module>
    main()
  File "/home/wdecoster/repositories/Clair3/clair3/../clair3.py", line 83, in main
    submodule.main()
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 945, in main
    CreateTensorFullAlignment(args)
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 723, in CreateTensorFullAlignment
    pos = next(samtools_pileup_generator)
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 661, in samtools_pileup_generator_from
    if hap in '12' and read_name_list[hap_idx] not in hap_dict:
IndexError: list index out of range
Calling variants ...
Total process positions in <chrom> : 0
Total time elapsed: 0.00 s
[INFO] No vcf output for file <path>/alignment_HP2/tmp/full_alignment_output/full_alignment_<chrom>.0_2.vcf, remove empty file
CreateTensor.py exited with exceptions. Exiting...
[INFO] Delay 6 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
  File "/home/wdecoster/repositories/Clair3/clair3/../clair3.py", line 89, in <module>
    main()
  File "/home/wdecoster/repositories/Clair3/clair3/../clair3.py", line 83, in main
    submodule.main()
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 945, in main
    CreateTensorFullAlignment(args)
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 723, in CreateTensorFullAlignment
    pos = next(samtools_pileup_generator)
  File "/home/wdecoster/repositories/Clair3/preprocess/CreateTensorFullAlignment.py", line 661, in samtools_pileup_generator_from
    if hap in '12' and read_name_list[hap_idx] not in hap_dict:
IndexError: list index out of range
Calling variants ...
Total process positions in <chrom> : 0
Total time elapsed: 0.00 s
[INFO] No vcf output for file <path>/alignment_HP2/tmp/full_alignment_output/full_alignment_<chrom>.1_2.vcf, remove empty file
CreateTensor.py exited with exceptions. Exiting...

real	0m33.027s
user	0m9.886s
sys	0m1.735s
cat: <path>/alignment_HP2/tmp/full_alignment_output/full_alignment_*.vcf: No such file or directory

Thanks,
Wouter

[Ruibang Luo]

Seems to be an error different from the last time. Yes please send me the logs at [e-mail].

[Wouter De Coster]

Fixed in the latest version, thanks @aquaskyline !

[Mariela Cortés López]

I am having the same issue with the version installed via bioconda.

[Ruibang Luo]

@mcortes-lopez probably not the same problem, if you can send me your logs, I can give them a check.