IndexError: list index out of range

[min0609]

Hi,

First of all, thank you for this wonderful tool.
I attempted to run a command to call somatic variants, but unfortunately, the command failed.
Could you please suggest a way to troubleshoot this error?

~/palmer_scratch/km/tools/lofreq_star-2.1.5_linux-x86-64/bin/lofreq somatic -n ~/palmer_scratch/km/ova_low_coverage/sample_05-S02_B/sample_05-S02_B.bam -t ~/palmer_scratch/km/ova_low_coverage/sample_05-S02_P/sample_05-S02_P.bam -l ~/palmer_scratch/km/ova_wes/ref/SureSelect_Human_All_Exon_V5.bed -f ~/palmer_scratch/km/ova_wes/db/human_g1k_v37_decoy.fasta --threads 8 -o sample_05-S02_ -d ~/palmer_scratch/km/ova_wes/db/dbsnp_137.b37.vcf.gz

CRITICAL [2023-10-18 06:49:50,574]: The following command failed with code 1: lofreq call-parallel --pp-threads 8 -d 101000 -f /home/jc2545/palmer_scratch/km/ova_wes/db/human_g1k_v37_decoy.fasta --verbose --no-default-filter -b 1 -l /home/jc2545/palmer_scratch/km/ova_wes/ref/SureSelect_Human_All_Exon_V5.bed -a 0.100000 --use-orphan -B -N -A /home/jc2545/palmer_scratch/km/ova_low_coverage/sample_05-S02_B/sample_05-S02_B.bam -o sample_05-S02_normal_relaxed.vcf.gz
CRITICAL [2023-10-18 06:49:50,574]: Received the following on stderr:
INFO [2023-10-18 06:49:49,659]: Using 8 threads with following basic args: lofreq call -d 101000 -f /home/jc2545/palmer_scratch/km/ova_wes/db/human_g1k_v37_decoy.fasta --verbose --no-default-filter -b 1 -a 0.100000 --use-orphan -B -N -A /home/jc2545/palmer_scratch/km/ova_low_coverage/sample_05-S02_B/sample_05-S02_B.bam

Traceback (most recent call last):

File "/vast/palmer/scratch/lifton/jc2545/km/tools/lofreq_star-2.1.5_linux-x86-64/bin/lofreq2_call_pparallel.py", line 744, in

main()

File "/vast/palmer/scratch/lifton/jc2545/km/tools/lofreq_star-2.1.5_linux-x86-64/bin/lofreq2_call_pparallel.py", line 593, in main

biggest = bins[-1]

IndexError: list index out of range

CRITICAL [2023-10-18 06:49:50,574]: Somatic SNV caller failed. Exiting

[andreas-wilm]

Could you please post the first two lines of the bed file here?

[min0609]

Here are the first ten lines of the bed file.

[andreas-wilm]

Hm. What does file ~/palmer_scratch/km/ova_wes/ref/SureSelect_Human_All_Exon_V5.bed return?

And could you also please share the output of samtools view -H /home/jc2545/palmer_scratch/km/ova_low_coverage/sample_05-S02_B/sample_05-S02_B.bam

Thanks

[min0609]

These are the outputs of the commands.

/home/jc2545/palmer_scratch/km/ova_wes/ref/SureSelect_Human_All_Exon_V5.bed: ASCII text

samtools_view_H.txt

The SureSelect_Human_All_Exon_V5.bed file was not used in GATK. Did this cause the error?

Thank you!

[andreas-wilm]

Unlikely. This all looks fine and I never came across this problem. If you could also share the full bed file then I can start debugging

[min0609]

SureSelect_Human_All_Exon_V5.txt

This is the BED file, and I converted it to a TXT format because BED format is not supported here.

[andreas-wilm]

Thanks. I still can't see anything unusual. Could you please just run the failing lofreq call command with lofreq call --verbose --debug -d 101000 -f /home/jc2545/palmer_scratch/km/ova_wes/db/human_g1k_v37_decoy.fasta --verbose --no-default-filter -b 1 -a 0.100000 --use-orphan -B -N -A /home/jc2545/palmer_scratch/km/ova_low_coverage/sample_05-S02_B/sample_05-S02_B.bam (with the added --debug flag) and share the output here?