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VGP / vgp-assembly

VGP repository for the genome assembly working group
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mitoVGP crashes on start #61

Closed mcurto closed 2 years ago

mcurto commented 2 years ago

Hi, when running mitoVGP for nanopore I am getting this error: scripts/mtDNApipe: 3: set: Illegal option -o pipefail scripts/blastMT: 3: set: Illegal option -o pipefail

Even when running the program with the test data: ./mitoVGP -a ONT -s Mastacembelus_armatus -i fMasArm1 -r mtDNA_Mastacembelus_armatus.fasta -t 24 -b variantCaller

Do you know what might be wrong? Thanks, Manuel

skoren commented 2 years ago

I'll guess you're on Ubuntu. There's an issue with Ubuntu where the default shell is dash and even scripts that have bash specified in the shebang run in dash which doesn't support pipe fail (see https://askubuntu.com/questions/886537/set-e-o-pipefail-not-working-on-bash-script-on-ubuntu-16 for example). Try running it as bash mitoVGP explicitly.

mcurto commented 2 years ago

Thanks Sergey. This means I will have to run each script individually, right? When I try to run bash mitoVGP I get the same error message.

skoren commented 2 years ago

It looks like mitoVGP itself launches jobs as sh scripts/mtDNApipe, etc. That is not correct since it uses bashisms so it should be bash scripts/mtDNApipe, etc. You should be able to update mitoVGP to use bash and I expect it will run. @gf777 you should update the repo to bash as well.

gf777 commented 2 years ago

right, better specify. I just did. Let me know if this fixes the issue