Issues with Mira

[amarth]

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.

[nickloman]

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.