I'm trying to use InParanoid (v4.1) to detect orthologs in two de novo transcriptomes I assembled. They were 'translated' to protein sequences using Transdecoder. The resulting fasta file I'm trying to use in InParanoid looks like this (~200 000 seqs):
I tried the example fasta files supplied with the program (called SC and EC) and it works, but when I use my files, it's stuck at the first step and it does not create any file (nor disk usage) after days. Here is what I get with my fasta files:
Loading module bio/ncbi-blast-2.2.22.
Formatting BLAST databases
Starting BLAST searches...
Starting first BLAST pass for bf - bf on [blastall] WARNING: the -C 3 argument is currently experimental
It then stays like this forever.
I also tried supplying my Blast results (inter-sample) generated myself that I parsed with their supplied parser but then it still stays forever at the same state, again without generating any file:
Done BLAST searches. Starting ortholog detection...
I tried with and without bootstraping, multitreading (-a16 option) or not, as I said with or without supplied blast results and I also cleaned my fasta files for any weird characters (removed annotations, all ' * ', spaces, empty lines and dots. Now I'm running out of ideas... I'm using a Unix cluster. I tried these jobs using up to 16 CPUs with 256G memory.
Anybody managed to make that program work?