run nextplolish2.py sleep
wang-zewen opened this issue · 8 comments
When running nextpolish2.py, the task remains in a sleep state after submission, and the thread count shows as 0.
nextpolish2.py -sp -p 10 -g input.genome.fasta -b input.genome.fasta.blc -i 1 -l lgs.sort.bam.list -r ont -o genome.nextpolish.part001.fasta
Try to kill it and rerun.
The reason for the process to sleep is that some contig cannot obtain the result during the execution of the line c_seq = P.ctg_cns_core(CFG, REFS.contents.ref[n], bam_list). How can we solve this problem?
Could you extract the sequences and bam of some contigs you mentioned and then send to me? so I can reprocude this bug.
https://drive.google.com/file/d/1Zb9nvHnpih3mr6_bjwvKODk3Ve1UOupN/view?usp=sharing
https://drive.google.com/file/d/1bqtCf9ghjbaKSw5G4Ajbxd7AbqvsPpPS/view?usp=sharing
you can download the error ctg file and bam file using the link
Thanks, but the bam file is too large to download, could you please extract the bam of the contigs that failed to polish. You can use samtools like this:
samtools view -b all.bam conitg_name > conitg_name.bam
The reads from your bam file contain lots of non-ATGC bases, so you need to remove these reads...
ok. Thank you.