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.
