failed log report
Closed this issue · 2 comments
I am sometimes getting a failed report for some of my scaffolds in some of my individuals. Not sure what is going on here;
021-09-08 13:45:38.945625: SNP calling completed for contig contig_109746. Time taken= 10.9951
2021-09-08 13:45:38.945724: ------WhatsHap SNP phasing log------
This is WhatsHap 1.0 running under Python 3.6.13
Working on 1 samples from 1 family
======== Working on chromosome 'contig_109746'
---- Processing individual SAMPLE
Using maximum coverage per sample of 15X
Number of variants skipped due to missing genotypes: 0
Number of remaining heterozygous variants: 3
Reading alignments and detecting alleles ...
Found 43 reads covering 3 variants
Kept 34 reads that cover at least two variants each
Reducing coverage to at most 15X by selecting most informative reads ...
Selected 15 reads covering 3 variants
Best-case phasing would result in 1 non-singleton phased blocks (1 in total)
... after read selection: 1 non-singleton phased blocks (1 in total)
Variants covered by at least one phase-informative read in at least one individual after read selection: 3
Phasing 1 sample by solving the MEC problem ...
MEC cost: 150
No. of phased blocks: 1
Largest component contains 3 variants (100.0% of accessible variants) between position 8310 and 9657
======== Writing VCF
Done writing VCF
== SUMMARY ==
Maximum memory usage: 0.203 GB
Time spent reading BAM/CRAM: 0.0 s
Time spent parsing VCF: 0.0 s
Time spent selecting reads: 0.0 s
Time spent phasing: 0.0 s
Time spent writing VCF: 0.0 s
Time spent finding components: 0.0 s
Time spent on rest: 0.3 s
Total elapsed time: 0.4 s
2021-09-08 13:45:45.886753: ------SNP phasing completed------
2021-09-08 13:45:45.886864: ------WhatsHap BAM phasing log------
Found 1 samples in input VCF
Keeping 1 samples for haplo-tagging
Found 0 samples in BAM file
Reading alignments and detecting alleles ...
Found 43 reads covering 3 variants
== SUMMARY ==
Total alignments processed: 189
Alignments that could be tagged: 72
Alignments spanning multiple phase sets: 0
haplotag - total processing time: 0.5968549251556396
2021-09-08 13:45:50.542123: ------BAM phasing completed-----
2021-09-08 13:45:50.542413: Indel calling started.
Traceback (most recent call last):
File "/n/home08/aggarner/NanoCaller/scripts/NanoCaller.py", line 257, in
run(args)
File "/n/home08/aggarner/NanoCaller/scripts/NanoCaller.py", line 115, in run
indel_vcf=indelCaller.test_model(in_dict, pool)
File "/n/home08/aggarner/NanoCaller/scripts/indelCaller.py", line 106, in test_model
for res in result:
File "/n/home08/aggarner/NanoCaller/scripts/generate_indel_pileups.py", line 328, in get_indel_testing_candidates
ref=''.join([ref_dict[p] for p in range(v_pos-window_before,v_pos+window_after+1)])
File "/n/home08/aggarner/NanoCaller/scripts/generate_indel_pileups.py", line 328, in
ref=''.join([ref_dict[p] for p in range(v_pos-window_before,v_pos+window_after+1)])
KeyError: 10410
Hi, thanks for pointing this out. The problem was with indels occurring near the end of contigs and I have updated the code to fix this issue. Please let me know if the latest commit fixes this issue on your end as well.
This seems to have fixed the error on my end.