Silent errors in logs #39
Description
Hello.
I’ve been running clairS-TO and noticed silent errors sometimes showing up in the logs at various steps. I haven’t been able to identify any patterns for when the errors show up.
I’m running it with the run_clairs_to wrapper script and hkubal/clairs-to:v0.3.1 container, on ONT long read data at a depth of 100x.
These are two examples I’ve come across:
[INFO] STEP 5: SNV VCF Post-processing
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs_to.py postprocess_vcf --ref_fn .../reference.fasta --pileup_vcf_fn .../snv_pileup_filtering.vcf --output_fn .../sample01.snv.vcf --platform ont --qual 35 --qual_cutoff_phaseable_region 35 --qual_cutoff_unphaseable_region 35 --sample_name sample01 --disable_indel_calling True --cmdline .../sample01/tmp/CMD ) 2>&1 | tee .../sample01/logs/5_PV_SNV.log
Warning: cannot find your CPU L2 cache size in /proc/cpuinfo
Traceback (most recent call last):
File "/opt/bin/clairs_to.py", line 110, in <module>
main()
File "/opt/bin/clairs_to.py", line 104, in main
submodule.main()
File "/opt/bin/src/postprocess_vcf.py", line 259, in main
merge_vcf(args)
File "/opt/bin/src/postprocess_vcf.py", line 111, in merge_vcf
pileup_vcf_reader.read_vcf()
File "/opt/bin/shared/vcf.py", line 242, in read_vcf
if columns[0][0] == "#":
IndexError: list index out of range
[INFO] STEP 4: Haplotype Filtering for SNV Variants
[INFO] RUN THE FOLLOWING COMMAND:
( pypy3 /opt/bin/clairs_to.py haplotype_filtering --tumor_bam_fn .../sample01/tmp/phasing_output/phased_bam_output/tumor_ --ref_fn .../reference.fasta --germline_vcf_fn .../sample01/tmp/vcf_output/snv_pileup.vcf --pileup_vcf_fn .../sample01/tmp/vcf_output/snv_pileup_nonsomatic_tagging.vcf --output_dir .../sample01/tmp/vcf_output --output_vcf_fn .../sample01/tmp/vcf_output/snv_pileup_filtering.vcf --samtools samtools --pypy3 pypy3 --parallel parallel --threads 4 --apply_haplotype_filtering True --disable_read_start_end_filtering True ) 2>&1 | tee .../sample01/logs/4_HAP_FILTER_SNV.log
Warning: cannot find your CPU L2 cache size in /proc/cpuinfo
Warning: cannot find your CPU L2 cache size in /proc/cpuinfo
Traceback (most recent call last):
File "/opt/bin/clairs_to.py", line 110, in <module>
main()
File "/opt/bin/clairs_to.py", line 104, in main
submodule.main()
File "/opt/bin/src/haplotype_filtering.py", line 906, in main
haplotype_filter_per_pos(args)
File "/opt/bin/src/haplotype_filtering.py", line 462, in haplotype_filter_per_pos
rb = reference_sequence[p - pos + flanking]
IndexError: string index out of range
Warning: cannot find your CPU L2 cache size in /proc/cpuinfo
Traceback (most recent call last):
File "/opt/bin/clairs_to.py", line 110, in <module>
main()
File "/opt/bin/clairs_to.py", line 104, in main
submodule.main()
File "/opt/bin/src/haplotype_filtering.py", line 906, in main
haplotype_filter_per_pos(args)
File "/opt/bin/src/haplotype_filtering.py", line 462, in haplotype_filter_per_pos
rb = reference_sequence[p - pos + flanking]
IndexError: string index out of range
Thanks!