Question: Why does abyss not produce contig files when I run in a loop on server
0
gravatar for getanid123
3 days ago by
getanid1230
getanid1230 wrote:

Hi all,

I was trying to run abyss 2.2.4 and I came across an issue. The loop includes running 5 kmers on 20 samples. The code used is as follows:

abyss-pe name='name' k='kmervalue' in = 'file1_r1.fq file1_r2.fq'

My loop is running fine and execute all 100 samples. But for 5 samples in between [not the extreme kmers or extreme samples in the list given to loop], some output files are not generated. I was wondering if I need to specify the thread parameter for abyss?

Please suggest!!

-Getan

abyss de novo assembly • 59 views
ADD COMMENTlink modified 3 days ago by lieven.sterck6.9k • written 3 days ago by getanid1230

What kind of output files are missing?

apart from the fact that for instance with certain kmers (or input) it can't get to an assembly result it should do the same for all samples.

ADD REPLYlink written 3 days ago by lieven.sterck6.9k

I was looking in particular for scaffolds and contigs files and they are not generated. But I was able to generate these files after running it again using same command line [outside loop].

ADD REPLYlink written 3 days ago by getanid1230

so this issue is (somewhat) resolved thus?

ADD REPLYlink written 3 days ago by lieven.sterck6.9k

It is a big task if I have to check all the samples for contigs.fa and regenerate all the missing contigs. I just wanted to know if I need to specify -np or -j parameters. I want to assign specific processes or threads to be on safe side.

ADD REPLYlink written 3 days ago by getanid1230
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