Open lfp-a opened 1 year ago
According to the error report result, "1.000 not in species map" appears, so it should be because of the problem in your input file that the number "1.000" is incorrectly identified as a species name. I think it is caused by the blank space in the cds or protein sequence name you input. PhyloMCL has strict requirements on this aspect (as it is packaged software, I cannot modify it). It is recommended that you try to repair it according to the following process;
If you do not want to repeat the first step of sequence alignment. You need to adjust the blastp sequence name of the "- in" file in "step2.sh", the sequence name and species name in "- species", and the species name in "- tree" to ensure that PhyloMCL runs successfully.
PS. In our experience, we generally pre process all sequence names as ">speciesnames_GeneID", which will facilitate later analysis.
Thank you for your help. I'll have a try
When I run step 2, I get an error. Here's what debug says
The following is the config setting
Thank you for your help