Question: Abyss Error when running Collector
0
gravatar for claire.morandin
7 days ago by
claire.morandin0 wrote:

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
abyss assembly • 64 views
ADD COMMENTlink modified 7 days ago by genomax46k • written 7 days ago by claire.morandin0

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.

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax46k

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.

ADD REPLYlink written 7 days ago by claire.morandin0

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

ADD REPLYlink written 7 days ago by genomax46k
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