Abyss Error when running Collector

Question

[claire.morandin]

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

[GenoMax]

Not sure if this will work but you may need to upgrade your version of zsh to v.5.0.8 or better. Or use a different shell like bash.

[claire.morandin]

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.

[GenoMax]

The version of zsh you have does not seem to support the option pipe fail, which is that the errors above is indicating.