[mira_talk] Re: gap2caf
- From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 12 Nov 2010 14:11:25 +0100 (MET)
I guess some non-allowed characters are present in the read names. Just to
check: can you send me the first 100 lines of the FASTA (or FASTQ) file you
used to assemble. Furthermore, the first 1000 lines of the CAF file in question?
Thanks,
B.
----- original message --------
Subject: [mira_talk] gap2caf
Sent: Fri, 12 Nov 2010
From: Brian Forde
Hello all,
I have edited a mira assembly in Gap and used gap2caf to convert back to a caf
file. As per the mira manual I then used convert_project to convert a caf to
maf with the -r switch to recalculate the consensus. However, i get the
following error
[0%] Read HWI-EAS210R_0001:5:103:1403:1164#GCCAAT/ already loaded before!
Fatal Error (may be due to problems of the input data):"Duplicate readname in
CAF file: HWI-EAS210R_0001:5:103:1403:1164#GCCAAT/"
->Thrown: Read & CAF::createCafRead()
->Caught: Error while creating CAF-Object.
Is there a simple fix for this problem?
regards
Brian
--- original message end ----
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