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Old 12-07-2012, 05:32 AM   #1
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 is offline   Reply With Quote

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