vg vg call - Segmentation fault (core dumped)

vg call - Segmentation fault (core dumped)

Open nklspp opened this issue 11 months ago • 6 comments

Hi VG teams I am copying a post from BioStars where I explain my process in more details but it was suggested to post the bug here. Here is the link from the original post.

1. What were you trying to do? I am trying to call variants using vg call using a previously built pangenome-graph. I build it using HGDP vcf and I am aligning other individuals from HGDP aswell.

2. What did you want to happen? I wanted to get a VCF from the GAM file that I got from the previous alignment step.

3. What actually happened? I have the following segmentation fault:

Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━
Crash report for vg
Crash report for vg ━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━
Crash report for vg ━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"

Crash report for vg ━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━
Crash report for vg
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━
Crash report for vg ━━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━
Crash report for vg ━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━
Crash report for vg ━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━
Crash report for vg ━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━
Crash report for vg ━
Crash report for vg ━━━━━━━━━━━━
Crash report for vg ━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━
Crash report for vg ━━━
Crash report for vg ━v1.48.0-59-g276aa51e3 "Gallipoli"
━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━
Crash report for vg ━━━━━━━━━━━
Crash report for vg ━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"

Crash report for vg ━━━
━━━━━━━━
Crash report for vg ━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"

v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━
Crash report for vg
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━
Crash report for vg ━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━
Crash report for vg
v1.48.0-59-g276aa51e3 "Gallipoli"
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Crash report for vg Crash report for vg ━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
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Crash report for vg ━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━━━Crash report for vg
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━v1.48.0-59-g276aa51e3 "Gallipoli"
━━v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━
Crash report for vg ━
Crash report for vg ━v1.48.0-59-g276aa51e3 "Gallipoli"
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Crash report for vg ━━━━━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━━━━━━━━━━
v1.48.0-59-g276aa51e3 "Gallipoli"
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
━
Crash report for vg v1.48.0-59-g276aa51e3 "Gallipoli"
v1.48.0-59-g276aa51e3 "Gallipoli"
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#0x1   Object "", at 0x1f8ec7b/cm/local/apps/slurm/var/spool/job2396054/slurm_script: line 25: 54161 Segmentation fault      (core dumped) vg call -t ${SLURM_CPUS_PER_TASK} FINALGRAPH/newxg.xg -k data/HGDP00607/concat.gam.pack > data/HGDP00607/HGDP00607_gam.vcf

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here: I am not too sure why my error message get multiple times the same error message (maybe due to the multithreading ?).

Stack trace (most recent call last) in thread 54597:

5. What data and command can the vg dev team use to make the problem happen?

vg construct -r ref.fa -v sub-chrXX.vcf.gz > pXX.vg
vg ids -j $(for i in $(seq 1 22); do echo p${i}.vg; done)
vg index -x all.xg $(for i in $(seq 1 22); do echo p${i}.vg; done)
vg prune -t 8 -k 45 -r p${SLURM_ARRAY_TASK_ID}.vg > pruned${SLURM_ARRAY_TASK_ID}.vg
vg index -t 8 --temp-dir temp -g wg.gcsa pruned{1..22}.vg -p -Z 32768 2>&1

From there I wanted concatenate my multiple forward reads using cat *1.fastq.gz > concatenated_1.fastq.gz and my reverse reads using cat *2.fastq.gz > concatenated_2.fastq.gz

From there I wanted to map my paired-end reads together as follow:

vg map -x all.xg -g wg.gcsa -f concatenated_1.fastq.gz -f concatenated_2.fastq.gz > HGDP00607.gam

HOWEVER I had the error : error [xg]: multiple hits for XXX that I am explaining in my BioStars post. So I ended up mapping my forward and reverse reads separately and concatenate them the gam in the next step:

vg map -x all.xg -g wg.gcsa -f HGDP00607/HGDP00607_1.fastq.gz > HGDP00607_1.gam
vg map -x all.xg -g wg.gcsa -f HGDP00607/HGDP00607_2.fastq.gz > HGDP00607_2.gam
cat *.gam > concat.gam
vg pack -x all.xg -g concat.gam -Q 1  -o concat.gam.pack
vg call all.xg -k concat.gam.pack > HGDP00607.vcf

And the error explained before is happening at the last vg call step.

At the same time, I was able to surject the gam file to a bam file and call the variant using HaplotypeCaller as follow:

vg surject -x all.xg -b concat.gam > concat.bam
samtools addreplacerg -r '@RG\tID:samplename\tSM:samplename' concat.bam -o concat_readgroup.bam
samtools sort concat_readgroup.bam > concat_readgroup_sorted.bam
samtools index concat_readgroup_sorted.bam
gatk HaplotypeCaller --input concat.bam --output HGDP00607_bam.vcf --reference ref.fa

The only error I encountered there was a warning: (warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths.) during the vg surject step.

6. What does running vg version say?

vg version v1.48.0-59-g276aa51e3 "Gallipoli"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux
Linked against libstd++ 20210601

EDIT: I also verified all .vg files using vg validate and they all returned valid.

Do you know where this segmentation fault can comes from ? I figured it might be an error from the indexes file but because it took us several month to run the index jobs on our HPC, I am trying to find a way to fix it without re-running those jobs.

Thanks !

Sep 04 '23 07:09 nklspp

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vg call - Segmentation fault (core dumped)

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