Stuck at step 2 (blast)
Hi,
I am running proteinortho v.6.3.1 with about 285000 protein sequences with command
proteinortho6.pl -project=MAGs ${DataDir}/*faa --cpus=24 --temp=$TMPDIR --clean
, where $DataDir is path to protein files. It is stuck at step 2 and here's the output after running for 3 days:
Step 2 using diamond Running blast analysis: 7.14% (704044/9859020)
Rerunning the job using same dmnd files for another 3 days slightly improved the progress from 7.14% to 8.7% (858513/9859020). I tried switching Blast alternative, MMseqs2, with --p=mmseqsp but it is still stuck at Step 2. I do have permission to write files in --temp dir, and I have tested with creating/deleting files.
I am wondering why it's taking forever to complete Diamond run. Thank you for your help and please let me know if you need any additional information.