prune_transcripts.py stucked

[xiaolichen0]

Hi Dr. Fields,

It seems prune_transcripts.py stucked at the Parsing sequence and count information step. I used -p 32 option. But after 1 or 2 minutes when I see "Parsing sequence and count information", Only 1 process is working and the cpu usage is nearly 0. I didn't see any error message in the output.

My bed12 file contains 200+ line. And prune_transcripts.py worked when I extracted the first 10 lines of the bed12 file. So I think the bam file and the fasta file should be fine. Do you have any idea what else can be wrong? Thanks in advance.

Best Regards,
Xiaoli

[D-Dinesh]

hi

could you please tell me which python scripts from ORF-Rater has to be run sequentially? I want to use ORF-Rater but I dont know where to start.

Thanks in advance