Comments (8)
Try to kill it and rerun.
from nextpolish.
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?
from nextpolish.
Could you extract the sequences and bam of some contigs
you mentioned and then send to me? so I can reprocude this bug.
from nextpolish.
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
from nextpolish.
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
from nextpolish.
Hi, This is the new file
https://drive.google.com/file/d/1K0meLhaBQ7rACd8tmNgL3lKdximk2fJ_/view?usp=sharing, https://drive.google.com/file/d/1MW0DbvsRzjehsHu1vj8EQSYLRBXK0dhX/view?usp=sharing, https://drive.google.com/file/d/1bqtCf9ghjbaKSw5G4Ajbxd7AbqvsPpPS/view?usp=sharing
from nextpolish.
The reads from your bam file contain lots of non-ATGC bases, so you need to remove these reads...
from nextpolish.
ok. Thank you.
from nextpolish.
Related Issues (20)
- Installation failure with multiple definition of 'rle_auxtab' HOT 3
- db_split failed: HOT 4
- How does NextPolish polish an assembly with long reads? HOT 1
- make[2]: *** [Makefile:30: bwa] Error 1 错误 HOT 1
- slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT HOT 1
- run fails with long read only in conda env HOT 5
- SLURM out of memory and time... HOT 1
- [main_samview] fail to read the header from "-" HOT 1
- zlib.h not found error HOT 1
- polish_genome failed HOT 1
- problem with NextPolish-CentOS6.9.tgz
- The process of polishing causes a significant decrease in genome size. HOT 8
- During the execution of samtools index, I encountered an error: "invalid option -- '@'" HOT 4
- An error message was encountered while running 00.lgs_polish/04.polish.ref.sh.work/polish_genome01
- How does NextPolish handle short-reads mapping to multiple parts of the genome? HOT 1
- The telemore sequences were removed after Nextpolish HOT 1
- After I run nextPolish run.cfg, the NextPolish vanished and generate a copy HOT 2
- After the gap filling for scaffolds, using NextPolish. HOT 1
- NextPolish fails with Short and Long Reads HOT 1
- NextPolish for metagenome? HOT 1
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