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Old 03-05-2013, 07:24 AM   #1
Location: Mexico City

Join Date: Dec 2012
Posts: 14
Unhappy Issues with Mira

Hi pals

Recently, my objective is to assemble some reads sequenced with Illumina/Solexa in fastq format (around 12 millions reads)...

I've chosen MIRA to make this work, i typed the command:

mira --project=assembly-H12-NoBackBone --job=denovo,genome,accurate,solexa
But unfortunately, i'm getting the next error:

Loading data from FASTQ file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.. zsh: killed
I've been reading about this 'zsh:killed' error, and found too little, as far as I understand, it seems that there's no error from MIRA but ZSH (or some linking program which MIRA uses)

Somebody knows how can I find that?

Additional Info: I'm using MIRA from the Bio-Linux repos, I'm going to compile by myself, maybe it should work.
amarth is offline   Reply With Quote
Old 03-05-2013, 07:32 AM   #2
Senior Member
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356

I would guess you are running up against a quota limit and your job is being killed by the shell. Try running ulimit -a and see whether there are strict user limits for your account. You may need to relax some, e.g. memory usage.
nickloman is offline   Reply With Quote

assembly, issue, mira, zsh

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