Hello,
I have been using Velvet to perform a denovo assembly and recently came across the Velvet Optimizer program that would help optimizing the input parameters for Velvet to perform a good assembly. I seem to be running into the same error while running Velvet Optimizer for the past few days.
I use the following command line to run the perl script:
VelvetOptimiser.pl -s 21 -e 91 -m 0.001 -o -exp_cov 0.000001 -f -bam /windows/D/genomes/macaca/paired_merged_Ig_TCR.bam -d /windows/D/genomes/macaca/Velvet_optimized
and the following error shows up:
Minimum specified coverage cutoff is higher than the expected coverage. Please choose a minimum coverage cutoff smaller than 0 and re-run.
I have tried several modifications (change m, the expected coverage, change the default values in the actual script) and different data sets, but I have not been able to proceed further/get rid of the error.
My background in linux/computer science is a month old, so my question might seem very basic and I apologize in advance. Any help would be appreciated Thanks in advance for your time!
I have been using Velvet to perform a denovo assembly and recently came across the Velvet Optimizer program that would help optimizing the input parameters for Velvet to perform a good assembly. I seem to be running into the same error while running Velvet Optimizer for the past few days.
I use the following command line to run the perl script:
VelvetOptimiser.pl -s 21 -e 91 -m 0.001 -o -exp_cov 0.000001 -f -bam /windows/D/genomes/macaca/paired_merged_Ig_TCR.bam -d /windows/D/genomes/macaca/Velvet_optimized
and the following error shows up:
Minimum specified coverage cutoff is higher than the expected coverage. Please choose a minimum coverage cutoff smaller than 0 and re-run.
I have tried several modifications (change m, the expected coverage, change the default values in the actual script) and different data sets, but I have not been able to proceed further/get rid of the error.
My background in linux/computer science is a month old, so my question might seem very basic and I apologize in advance. Any help would be appreciated Thanks in advance for your time!
Comment