Question: Orthofinder producing thousands of files?
gravatar for nickchristodoulides3
3.6 years ago by
nickchristodoulides30 wrote:


I am trying to get a multiple sequence alignment from 60 insect transcriptomes. I have performed the first part of orthofinder on my BLAST results directory, and now have orthogroups. However, when trying to complete the rest of the process, using the -fg option to get a MSA, the results directory with Gene_distances and Trees have hundreds of thousands of files in them, so I exceed my file quota limit on my server. Is there any way to reduce the number of files created? Are there supposed to be that many files? Also, before I hit my file limit, I got a series of errors such as:

Error: Cannot open file 'OG0167322.phy_fastme_stat.txt'

Any suggestions as to how to not exceed file limit?

orthofinder • 952 views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 3.6 years ago by nickchristodoulides30
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