about the bug in nextdenovo2.0

[nextomics]

about the bug in nextdenovo2.0

[moold]

Could you paste the get cns log in here?

[wangzhongkai1]

hostname

• hostname
  cd /share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns00
• cd /share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/02.cns_align/01.get_cns.sh.work/get_cns00
  time python /share/home/ryd/bin/NextDenovo-2.0/lib/nextcorrect.py -f /share/home/ryd/xyjj/01_nextdenovo-2.0/./01_rundir/02.cns_align//01.get_cns.input.idxs -i /share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.013.sorted.ovl -p 8 -max_lq_length 10000 -o cns.fasta;
• python /share/home/ryd/bin/NextDenovo-2.0/lib/nextcorrect.py -f /share/home/ryd/xyjj/01_nextdenovo-2.0/./01_rundir/02.cns_align//01.get_cns.input.idxs -i /share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.013.sorted.ovl -p 8 -max_lq_length 10000 -o cns.fasta
  [INFO] 2019-10-28 11:40:37,316 Corrected step options:
  [INFO] 2019-10-28 11:40:37,317 Namespace(blacklist='/share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.013.sorted.ovl.bl', dbuf=False, fast=False, idxs='/share/home/ryd/xyjj/01_nextdenovo-2.0/./01_rundir/02.cns_align//01.get_cns.input.idxs', max_cov_aln=130, max_lq_length=10000, min_cov_base=4, min_cov_seed=10, min_error_corrected_ratio=0.8, min_len_aln=500, min_len_seed=10000, out='cns.fasta', ovl='/share/home/ryd/xyjj/01_nextdenovo-2.0/01_rundir/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.013.sorted.ovl', process=8, split=False)
  [WARNING] 2019-10-28 11:40:37,397 Skip 47571 seeds in blacklist.
  [INFO] 2019-10-28 11:40:37,797 Start a cns worker in 19860 from parent 19849
  [INFO] 2019-10-28 11:40:37,798 Start a cns worker in 19864 from parent 19849
  [INFO] 2019-10-28 11:40:37,798 Start a cns worker in 19862 from parent 19849
  [INFO] 2019-10-28 11:40:37,799 Start a cns worker in 19866 from parent 19849
  [INFO] 2019-10-28 11:40:37,800 Start a cns worker in 19867 from parent 19849
  [INFO] 2019-10-28 11:40:37,801 Start a cns worker in 19869 from parent 19849
  [INFO] 2019-10-28 11:40:37,802 Start a cns worker in 19873 from parent 19849
  [INFO] 2019-10-28 11:40:37,803 Start a cns worker in 19871 from parent 19849
  [INFO] 2019-10-28 14:37:27,045 Start a cns worker in 20875 from parent 19849

[moold]

The log shows a thread has crashed maybe because of a known bug, I plan to release the next version and fix it in this week.

[wangzhongkai1]

Bingo, thank you.

[zijiangyang]

@moold
Hi Hu:
I got the same error on one project but the nextdenovo works perfectly for several other genome assembly projects. The settings in run.cfg for these projects are exactly the same. May I ask is this error related to the input data?

Many thanks!

[moold]

In some extent, yes. This bug will be triggered only if a seed contains lots of low quality regions. I will fix it in the next release.

[zijiangyang]

In some extent, yes. This bug will be triggered only if a seed contains lots of low quality regions. I will fix it in the next release.

That would be great! Really appreciate your effort in developing this amazing software!

[moold]

Hi, you can try to download the latest version and this bug has been fixed.

[wangzhongkai1]

Dear Hu,
Glad to tell tou that the program has been normally finished, thanks for your effort!