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PBcR does not render any overlaps

I ran PBcR on simulated Pacbio reads but the asm.ovlStore.err has the following info:

Scanning overlap files to count the number of overlaps.
WARNING:  No overlaps found (or file not found) in 'home/PBcR/tempNA/./1-overlapper/001/000001.ovb'.
Found 0.000 million overlaps.

Since this is a simulated data, I use libraryname NA, as shown in the command below. There should be lots of overlaps. Is there anything wrong in the command? Thanks to anyone who could help on this question!

PBcR -s pacbio.spec -libraryname NA -fastq simulation.fq
assembly
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updated by Ram Ram • written by xianfan.jhu • xianfan.jhu

1 answer

This has been fixed. I added the options of -length, -genomeSize, -maxCoverage and -coverageCutoff, and now it renders overlaps.

• 0 views • link
updated by Ram Ram • written by xianfan.jhu • xianfan.jhu

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