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Prefix with dash needs quotes in velveth command line #4
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Can you show us the full command? I just tested this with Velvet and VelvetOptimiser and I cannot reproduce the error. |
Upon further inspection, I can confirm this is a bug in VelvetOptimiser. I was running VelvetOptimiser from a git branch where I have made a number of changes to the code (mentioned in a previous issue report), and this is one of the things I fixed long ago but forgot about it. The other solution is to just replace dashes with underscores and you won't get this issue. |
Thanks for the reply, I was scratching my head what else I could have done wrong in my pipeline. Changing only the line I mentioned caused the expected coverage optimization at the end to not start at all, so my one line fix was a bit naïve. I am glad you fixed the problem. |
You should use this branch for the bug fixes (I haven't touched the master branch yet): https://github.com/sestaton/VelvetOptimiser/tree/topic/reuse_sequences I should mention that currently the dashes are replaced with underscores because I never had a situation where it was critical. So, if you specify |
When using the option -p with a dash in the string, I get strange error messages about wrong category numbers. For example with LTCF-1-10:
After a lot of trial and error I could trace it back to dashes in the prefix. By putting single quotes around the prefix in line 546 I got rid of the error:
I think the problem lies in velvet itself, but am not sure.
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