almreis
commented
3 months ago Sorry, this was resolved by excluding the --skip-assembly option
Closed almreis closed 3 months ago
almreis
commented
3 months ago Sorry, this was resolved by excluding the --skip-assembly option
I'm encountering a segmentation fault when running LongTR with phased BAM tags to genotype and phase TRs. Below are the details of the command used and the error message.
DIR=test_data ./LongTR --bams ${DIR}/HG002_sample_reads.bam,${DIR}/HG003_sample_reads.bam,${DIR}/HG004_sample_reads.bam \ --fastahg38.analysisSet.fa \ --regions ${DIR}/test_regions_hg38.bed \ --tr-vcf test.vcf.gz \ --bam-samps HG002,HG003,HG004 --bam-libs HG002,HG003,HG004 \ --min-reads 5 \ --max-tr-len 10000 \ --skip-assembly \ --phased-bam
`Using phased BAM tags to genotype and phase TRs (WARNING: Any arguments provided to --snp-vcf will be ignored) Detected 3 BAM/CRAM files User-specified read groups for 3 unique samples Reading region file /g/data/if89/testdir/LongTR_v2/LongTR/test_data/test_regions_hg38.bed Region file contains 40 regions
Processing region chr1 776604 776633 90 reads overlapped region, of which 0 were hard clipped 0 had an 'N' base call 0 had low MAPQ 2 had low base quality scores 1 did not span the STR 0 did not have a unique mapping 87 PASSED ALL FILTERS Skipping phasing information for sample HG004 as there was many unphased reads. Skipping phasing information for sample HG002 as there was many unphased reads. Phased SNPs add info for 0 out of 87 reads Trimming reads Failed to trim align 1 out of 87 reads Generating candidate haplotypes TCTAGCCTGGGTGACAATAGAAAGACTCCATCTCA AAAACAAAACAAAACAAAACAAAACAAAA AACCACTAAAAAAAAGACTCCATTTCAAAAACAAA Added 0 inexact haplotypes generated by POA Aligning reads to each candidate haplotype Processing flanking sequences Segmentation fault`
System Information
Running some debugging, this is where the error seems to happen:
0 0x0000000000012cf0 __funlockfile() :0 1 0x0000000000463223 SeqStutterGenotyper::assemble_flanks() /g/data/if89/testdir/LongTR_v2/LongTR/src/seq_stutter_genotyper.cpp:107 2 0x0000000000464e33 SeqStutterGenotyper::genotype() /g/data/if89/testdir/LongTR_v2/LongTR/src/seq_stutter_genotyper.cpp:664 3 0x000000000047b691 GenotyperBamProcessor::analyze_reads_and_phasing() /g/data/if89/testdir/LongTR_v2/LongTR/src/genotyper_bam_processor.cpp:296 4 0x000000000047015b SNPBamProcessor::process_phased_reads() /g/data/if89/testdir/LongTR_v2/LongTR/src/snp_bam_processor.cpp:236 5 0x000000000044dc31 BamProcessor::process_regions() /g/data/if89/testdir/LongTR_v2/LongTR/src/bam_processor.cpp:626 6 0x000000000044dc31 ???() /apps/gcc/10.3.0/include/c++/10.3.0/bits/basic_string.h:222 7 0x000000000044dc31 ???() /apps/gcc/10.3.0/include/c++/10.3.0/bits/basic_string.h:231 8 0x000000000044dc31 ???() /apps/gcc/10.3.0/include/c++/10.3.0/bits/basic_string.h:658 9 0x000000000044dc31 ???() /g/data/if89/testdir/LongTR_v2/LongTR/src/region.h:66 10 0x000000000044dc31 BamProcessor::process_regions() /g/data/if89/testdir/LongTR_v2/LongTR/src/bam_processor.cpp:595 11 0x000000000041356e main() /g/data/if89/testdir/LongTR_v2/LongTR/src/hipstr_main.cpp:582 12 0x000000000003ad85 __libc_start_main() ???:0 13 0x00000000004160ae _start() ???:0