VelvetOptimiser offering different results on galaxy vs command line

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.


My guess is that the underlying tool versions differ. Or, maybe there is some bug.

The version of this tool and the resource allocated are intended for very small tutorial-sized datasets when working at public Galaxy servers. Some servers even have the tool marked as deprecated. The last wrapper update was in 2021, details: Galaxy | Tool Shed. If you want to help us to fix the wrapper, the development repository is linked from there.

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