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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Unexplained status when I run #73

Closed Weihankk closed 4 years ago

Weihankk commented 4 years ago

Hi, yesterday I used NextDenovo v2.3.0 to assemble my Pacbio data. Everything is fine at the beginning. But after ctg_algin it seems stop without any information. I can found some process by ps, and some ctg_cns.py process show status S+.

I suspect it is a problem with my computer, so I tried two times in different node. Unfortunately, both of them showed the same problem. What's even stranger is that in my seconde test in another node it cause many zombie process (status : Z ).

Here are screenshots of my problem:

The first time I tried on my node2, it has 256G RAM and 40 threads, disk space is enough to store the process files. I run this task in three days ago. When I found it seems stop so I uss ctrl+C to stop it. Now I find some zombie process. image

Yesterday morning I trid the second time to run it. I change to node3, it has 512G RAM and 88 threads. It seems stop now: image

Many ctg_cns.py process showed S+ image

RAM is not used. image

top command showed no process, either. image

Here is my run.cfg. image

In addition, the genome size I assemble is about 250MB, a plant. I input two fasta format file , about 130X pacbio data.

Thank for your help. If you need additional information or testing, please contact me.

moold commented 4 years ago
  1. change -x ava-ont to -x ava-pb if you used the PacBio data.
  2. change pa_correction to 3.
Weihankk commented 4 years ago

Thank you. It's running correctly now.