Question: Abyss Error when running Collector
0
gravatar for claire.morandin
3 months 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 • 159 views
ADD COMMENTlink modified 3 months ago by genomax51k • written 3 months 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 3 months ago • written 3 months ago by genomax51k

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 3 months 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 3 months ago by genomax51k
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