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?