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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg deconstruct got error for a specific path #3755

Open ZoeYang2020 opened 2 years ago

ZoeYang2020 commented 2 years ago

1. What were you trying to do? Use vg deconstruct a gfa file into vcf file

2. What did you want to happen? get a list a vcf file

3. What actually happened? libgomp: libgomp: Thread creation failed: Resource temporarily unavailable

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: Crash report for vg v1.41.0

Place stacktrace here.


**5. What data and command can the vg dev team use to make the problem happen?**
https://github.com/ZoeYang2020/Pangenome-graph-for-bacterial-pathogens/blob/main/minigraph_cactus_inversion/3bovis_restart4_20k95.gfa

vg deconstruct -p NC_014760.1 -a -e -K  3bovis_restart4_20k95.gfa> 3bovis_restart4_20k95_aeK_path1.vcf

if I use another path, it works. 
vg deconstruct -p NC_015725.1 -a -e -K  3bovis_restart4_20k95.gfa> 3bovis_restart4_20k95_aeK_path2.vcf

**6. What does running `vg version` say?**

Place vg version output here

Hendricks27 commented 1 year ago

I hit the same issue with the newest version (1.49), the previous version (1.48) was fine. But I was running it in a official ubuntu docker container within LSF/bsub system.