VelvetOptimiser can't go further
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Entering edit mode
5.2 years ago
Xin ▴ 70

Dear all,

I used Trinity to assemble my reads before. Now I'd like to assemble those reads with another tools such as Velvet/Oases. I tried to use VelvetOptimiser to find out optimized kmer and other parameters. But every time I run the program It stops in a specific line. It does not give any error, just nothing happens anymore.

This is the code I use: /home/Bioinfo/SW/velvet-master/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl -s 32 -e 73 -x 17 -f '-shortPaired -fastq ACDshuffeled.fq'

At first, I thought it might be due to lack of free space but know I have 817 GB free. I reduced the number of Kmers to only 4 kmers (32, 47, 63, 73) to reduce the number of assemblies should be done at once but I still can't get any result. Size of the folder(which contains sub-folders generated by velvetoptimiser) also does not change anymore.

Every time it can't go further than this line: Wide character in print at /home/Bioinfo/SW/velvet-master/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl line 735, <in> line 11011984.

I appreciate any suggestion to solve this issue.

RNA-Seq • 1.2k views
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