umahsn
commented
2 years ago 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.
aguygarner
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:
ref=''.join([ref_dict[p] for p in range(v_pos-window_before,v_pos+window_after+1)])
KeyError: 10410
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