vg deconstruct libgomp: Thread creation failed: Resource temporarily unavailable

[Wwwwwwwyc]

Hi！ I built the graph with 9 samples, however I got the following error when I used more samples.

This is my pipeline pggb -i all.fasta -o ../pggb/ -n 34 -t 48 -p 90 -s 5000 -S -m -V 'ref:#'

[vg::deconstruct] making VCF with reference=ref and delim=#

libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: 
libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailableThread creation failed: Resource temporarily unavailable

Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable

libgomp: 
libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable

libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
Command exited with non-zero status 1
vg deconstruct -P ref -H # -e -a -t 64 ../pggb//all.fasta.95c7b37.417fcdf.afa09f8.smooth.final.gfa
486.65s user 7.81s system 108% cpu 456.94s total 1866512Kb max memory

[AndreaGuarracino]

@Wwwwwwwyc, I've never seen such an error. Are you working on an HPC? About vg, we just download the static binary of it, so it could be that something is missing on your system. The error message shows that vg was unable to create a new thread due to a lack of resources.

[Wwwwwwwyc]

Thanks for your help! I didn't work on HPC. I then tried downloading the latest version of VG to complete the deconstruct. A few days later, I also completed the deconstruct using VG in PGGB, but I wasn't quite sure why I was getting this error.

[AndreaGuarracino]

Hope this error will never pop up again! xD