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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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segmentation fault #48

Open boyangzhao opened 3 years ago

boyangzhao commented 3 years ago

I'm getting a segmentation error when I ran HLA-LA at the --action HLA step. The stdout just says run was unsuccessful. If I run the part ./bin/HLA-LA --action HLA... specifically, I get that it failed, it just outputs Segmentation fault. This is with my own bam file. I cannot get the example NA12878.mini.cram to work, as it couldn't even get past the picard step, there I got the SAM validation error bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned.

Tool versions HLA-LA 1.0.1 samtools 1.10 picard 1.123 bwa 0.7.17 bamtools 2.5.1 boost 1.59.0

Log

Identified paths:
    samtools_bin: /opt/samtools/bin/samtools
    bwa_bin: /opt/bwa
    java_bin: /usr/bin/java
    picard_sam2fastq_bin: /opt/picard_tools/SamToFastq.jar
    General working directory: /hla-la
    Sample-specific working directory: /hla-la/test

Extract reads from 2 regions...
Extract unmapped reads...
Merging...
[bam_translate] RG tag "1" on read "A00609:45:HW72GDSXX:3:1101:28800:29105" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "A00609:45:HW72GDSXX:3:1101:28800:29105" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
Indexing...
Extract FASTQ...
    /usr/bin/java -Xmx10g -XX:-UseGCOverheadLimit -jar /opt/picard_tools/SamToFastq.jar VALIDATION_STRINGENCY=LENIENT I=/hla-la/test/extraction.bam F=/hla-la/test/R_1.fastq F2=/hla-la/test/R_2.fastq FU=/hla-la/test/R_U.fastq 2>&1

Now executing:
../bin/HLA-LA --action HLA --maxThreads 1 --sampleID test --outputDirectory /hla-la/test --PRG_graph_dir /opt/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT --FASTQU /hla-la/test/R_U.fastq.splitLongReads --FASTQ1 /hla-la/test/R_1.fastq --FASTQ2 /hla-la/test/R_2.fastq --bwa_bin /opt/bwa --samtools_bin /opt/samtools/bin/samtools --mapAgainstCompleteGenome 1 --longReads 0
Set maxThreads to 1
HLA-LA execution not successful. Command was ../bin/HLA-LA --action HLA --maxThreads 1 --sampleID test --outputDirectory /hla-la/test --PRG_graph_dir /opt/HLA-LA/src/../graphs/PRG_MHC_GRCh38_withIMGT --FASTQU /hla-la/test/R_U.fastq.splitLongReads --FASTQ1 /hla-la/test/R_1.fastq --FASTQ2 /hla-la/test/R_2.fastq --bwa_bin /opt/bwa --samtools_bin /opt/samtools/bin/samtools --mapAgainstCompleteGenome 1 --longReads 0
AlexanderDilthey commented 11 months ago

Hi @boyangzhao,

Could you provide a BAM to reproduce the issue?