Comments (4)
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.
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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.
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right, better specify. I just did. Let me know if this fixes the issue
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Related Issues (20)
- time of running MITOVGP HOT 36
- how to use DNAnexus Workflow to assembly genome HOT 4
- Sex chromosome assembly HOT 3
- Chromosome status estimation HOT 8
- error in Asset HOT 3
- 10X align HOT 3
- genomescope evaluation HOT 7
- asset bionano problem HOT 2
- mitoVGP crashes on start HOT 8
- QUESTION: Does mitoVGP need pacbio RAW data (BAM) files as input? HOT 3
- mitovgp trimmer failing HOT 2
- plant mitochondrial genomes? HOT 6
- Runtime? HOT 1
- Clarification in documentation: Polishing phased assemblies HOT 4
- Possible missed documentation -- haplotype merging step HOT 4
- Pipeline for Polishing Canu assembly with Illumina Reads HOT 1
- Problem install conda environment HOT 4
- BLAST options error: File .fasta does not exist HOT 11
- telomere prediction HOT 1
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