meta-velvetg cannot detect peak errors

[plumb]

I am running my illumina data using metavelvet. I got the following message. Anybody has experiences with that?

Thank you in advance.

Writing into graph file k51/Graph...
WARNING: NO COVERAGE CUTOFF PROVIDED
Velvet will probably leave behind many detectable errors
See manual for instructions on how to set the coverage cutoff parameter
Writing into stats file k51/stats_EstimateCovMulti.txt...
Starting peak detection...
Error!! Couldn't detect any peaks

[seb567]

I am running my illumina data using metavelvet. I got the following message. Anybody has experiences with that?

Thank you in advance.

Writing into graph file k51/Graph...
WARNING: NO COVERAGE CUTOFF PROVIDED
Velvet will probably leave behind many detectable errors
See manual for instructions on how to set the coverage cutoff parameter
Writing into stats file k51/stats_EstimateCovMulti.txt...
Starting peak detection...
Error!! Couldn't detect any peaks

First, you can try with a lower value for the k-mer length.

51 is very high -- Velvet does not correct your reads for errors. Therefore, most of your k-mers will likely have a depth of 1 or 2.

I suggest you try 21 as a test.


Also, you won't have any peak in most real metagenomes.




We use Ray to assemble gut microbiomes and it works well.

How to use Ray:

mpiexec -n 64 Ray \
 -k \
 31 \
 -p \
 Sample/ERR011142_1.fastq.gz \
 Sample/ERR011142_2.fastq.gz \
 -p \
 Sample/ERR011143_1.fastq.gz \
 Sample/ERR011143_2.fastq.gz \
 -o \
 Assembly

Sébastien Boisvert