Abyss Error when running Collector
Hello,
I am trying to run Kollector, an assembly software that uses Abyss. I run into an error that I do not understand so far, so I was hoping someone would know
Thank you for your help
> kollector.sh: 596.52 kollector-recruit.mk name=kollector seed=kollector_reference.fa pe1=Aquilonia_1.fastq pe2=Aquilonia_2.fastq s=0.50 r=0.7 n=10000 j=1 k=25
> Running ABySS
> assembly... zsh: no such option: pipe fail
> zsh: no such option: pipe fail
> zsh: no such option: pipe fail
> zsh: no such option: pipe fail
> zsh: no such option: pipe fail
> make: Entering directory `./Genomes_new/Kollector/Subset/Aquilonia/kollector.abyss'
> mpirun -np 1 ABYSS-P -k32 -q3 -v --coverage-hist=coverage.hist -s kollector-bubbles.fa -o kollector-1.fa ../kollector.recruited_pe.fastq
> zsh: no such option: pipefail make:
> *** [kollector-1.fa] Error 1
> make: Leaving directory `./Genomes_new/Kollector/Subset/Aquilonia/kollector.abyss'
> kollector.sh: 0.01 abyss-pe -C kollector.abyss v=-v k=32 name=kollector np=1 lib=pet pet=../kollector.recruited_pe.fastq long=longlib longlib=../kollector_reference.fa
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GenoMax
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claire.morandin •
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claire.morandin •
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Not sure if this will work but you may need to upgrade your version of
zshto v.5.0.8 or better. Or use a different shell likebash.Thank you for your reply, I think the zsh is not really the problem, if Abyss does not find my zsh file, it will automatically fall back on the bash file, which it does.
The version of
zshyou have does not seem to support the optionpipe fail, which is that the errors above is indicating.