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Old 12-07-2012, 05:32 AM   #1
magarolo
Junior Member
 
Location: Köln, Germany

Join Date: Aug 2011
Posts: 4
Default RNA-Seq de novo assembly Velvet, erros in multi-kmers

Dear All,

I am a new user of Velvet/Oases. Probably, this is trivial for some of you, but I would really appreciate, if I can get a hint to solve my error.

I am using paired-end reads in a bam format. My file contain the unmapped reads generated by TopHat.

The code that I used is...
velveth outdir 15,31,2 -bam -short file_rep1.bam file_rep2.bam

but my program fails giving me this error

Done inputting sequences
[3204.203284] Destroying splay table
[3204.818570] Splay table destroyed
ln: creating symbolic link `outdir/_17/Sequences': File exists
[3205.417374] Reading read set file outdir/_17/Sequences;
[3232.888105] 86263142 sequences found
[3389.408883] Done
[3389.408937] 86263142 sequences in total.
velveth: Couldn't write to file Sequences/Roadmaps: No such file or directory

The files Sequences and Roadmaps exist in the _15 folder that was created by Velvet. Should I move these file into the general folder outdir so the program can continue with the computation and why is this error happening?

Many thanks for your help in advance,

magarolo
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