IndexError: list index out of range

[santoshe1]

Hello,

I am running Straglr for multiple samples and one of the samples is unsuccessful with the below error:

Command

python straglr.py <sample.bam> <ref.fna>

Error:

Aug 04, 2023 10:00:57:IndexError: list index out of range
Aug 04, 2023 10:00:57:    allele1_repeat_count = round(cols[5])
Aug 04, 2023 10:00:57:  File "/root/miniconda3/envs/straglr/lib/python3.10/site-packages/straglr/tre.py", line 1259, in output_vcf
Aug 04, 2023 10:00:57:    tre_finder.output_vcf(variants, args.vcf, args.sample, args.loci)
Aug 04, 2023 10:00:57:  File "/root/miniconda3/envs/straglr/lib/python3.10/site-packages/straglr/straglr_genotype.py", line 78, in main
Aug 04, 2023 10:00:57:    sys.exit(main())
Aug 04, 2023 10:00:57:  File "/root/miniconda3/envs/straglr/bin/straglr-genotype", line 8, in <module>
Aug 04, 2023 10:00:57:Traceback (most recent call last):
Aug 04, 2023 10:00:50:IndexError: list index out of range
Aug 04, 2023 10:00:50:    allele1_repeat_count = round(cols[5])
Aug 04, 2023 10:00:50:  File "/root/miniconda3/envs/straglr/lib/python3.10/site-packages/straglr/tre.py", line 1259, in output_vcf
Aug 04, 2023 10:00:50:    tre_finder.output_vcf(variants, args.vcf, args.sample, args.loci)
Aug 04, 2023 10:00:44:  File "/root/miniconda3/envs/straglr/lib/python3.10/site-packages/straglr/straglr_genotype.py", line 78, in main
Aug 04, 2023 10:00:44:    sys.exit(main())
Aug 04, 2023 10:00:44:  File "/root/miniconda3/envs/straglr/bin/straglr-genotype", line 8, in <module>
Aug 04, 2023 10:00:44:Traceback (most recent call last):

Could you please let me know if the reason is no TR available? I see one similar issue reported on your Git page?

[readmanchiu]

Looking at the traceback it points to a script/module called straglr_genotype.py or straglr-genotype, something not in the current repository. It might be something I wrote before and removed, or it might be some wrapper other people wrote? Are you sure you are running the latest version from our repository?

[santoshe1]

Yes. I am running a wrapper from https://github.com/philres/straglr. Could the index out of range be due to lack of TRs.

[readmanchiu]

It could be, but it could also be one problematic locus that aborted the program. I would recommend you run the latest version in our repo to see if there is any problem.