Running VG deconstruct failed in the gfa generated from PGGB pipline

[isaamael]

1. What were you trying to do?

Use vg deconstruct to generate vcf from the gfa produced by the PGGB pipeline.

2. What did you want to happen? The PGGB runs by chromosome, and each chromosome should produce a vcf file

3. What actually happened? Some chromosomes run successfully and produce results, while some chromosomes fail and report errors.

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:

ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!
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#1    Object "/public/home/xuruiqiang/software/vg/vg", at 0x20757d5, in raise
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
#3    Object "/public/home/xuruiqiang/software/vg/vg", at 0x5e5053, in __assert_fail_base.cold
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
#2    Object "/public/home/xuruiqiang/software/vg/vg", at 0x5e512b, in abort
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
##3    Object "/public/home/xuruiqiang/software/vg/vg", at 0x5e5053, in __assert_fail_base.cold
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"

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Crash report for vg v1.50.1 "Monopoli"
#1    Object "/public/home/xuruiqiang/software/vg/vg", at 0x20757d5, in raise
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
#1    Object "/public/home/xuruiqiang/software/vg/vg", at 0x20757d5, in raise
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
1    Object "/public/home/xuruiqiang/software/vg/vg", at 0x20757d5, in raise
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
3    Object "/public/home/xuruiqiang/software/vg/vg", at 0x5e5053, in __assert_fail_base.cold
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
Stack trace (most recent call last) in thread 36073:
#24   Object "", at 0xffffffffffffffff, in 
Stack trace (most recent call last)/var/spool/slurm/d/job15597806/slurm_script: line 21: 35163 Segmentation fault      (core dumped) /public/home/xuruiqiang/software/vg/vg deconstruct --all-snarls -P TS --threads 10 $pggbdir/in.fa.gz.e316b50.community.3.fa.out/in.fa.gz.e316b50.community.3.fa.e316b50.417fcdf.7fecd6e.smooth.final.gfa > $outdir/3.vcf

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

6. What does running vg version say?

/public/home/xuruiqiang/software/vg/vg version

vg version v1.50.1 "Monopoli"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Built by anovak@emerald