Hello,
My VelvetOptimiser is offering different results on galaxy vs. my command line.
Here are the inputs i used on galaxy:
and this is from my command line
VelvetOptimiser.pl -s 55 -e 69 -x 2 -f '-shortPaired -fastq -separate trial2.trimmed.paired.R1.fastq trial2.trimmed.paired.R2.fastq' -f '-short -fastq trial2.trimmed.unpaired.R1.fastq' -f '-short -fastq trial2.trimmed.unpaired.R2.fastq'
(trial2.trimmed.paired.r1…unpaired.R2.fastq are the same post-trimming files as the ones on galaxy)
For velvet, I cloned the github repo using
git clone https://github.com/dzerbino/velvet.git
and compiled it to make the MAXKMERLENGTH = 121 with the command
make 'MAXMAXKMERLENGTH = 121'
I’ve troubleshooted quite a bit, beginning with the swapping of the format and type as per the github.
VelvetOptimiser.pl -s 55 -e 69 -x 2 -f '-fastq -shortPaired -separate trial2.trimmed.paired.R1.fastq trial2.trimmed.paired.R2.fastq' -f '-fastq -short trial2.trimmed.unpaired.R1.fastq' -f ' -fastq -short trial2.trimmed.unpaired.R2.fastq'
I also made sure to add the velvet folder and folder containing velvet optimiser to my path.
Any ideas what I’m doing wrong? I attached pictures of my error file if that helps; any feedback would be greatly appreciated.