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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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Non-zero exit status 134 #167

Open FabianDK opened 1 year ago

FabianDK commented 1 year ago

Dear Devs,

I am running NextDenovo (v2.5.0) on a 2.4Gb mammalian genome using Nanopore data in Docker with Ubuntu 20.04.2 LTS and Python 3.10.6 in a Nextflow pipeline (allocated cpus = 16, memory = 286.GB).

The requirements were installed like this in docker:

RUN git clone https://github.com/moold/ParallelTask && cd ParallelTask && git reset --hard ffd4e15afb5f4a450c46b766bb02763d648c187d && pip install .
RUN wget https://github.com/Nextomics/NextDenovo/releases/download/v2.5.0/NextDenovo.tgz --no-check-certificate && tar -vxzf NextDenovo.tgz && cd NextDenovo && cd / && rm NextDenovo.tgz

Soon after "[39 INFO] 2023-02-19 07:55:52 raw_align done", I am getting "returned non-zero exit status 134". Please see the log file here: command.log

If this is a resource issue, I have followed the resource optimization guideline here: https://nextdenovo.readthedocs.io/en/stable/FAQ.html#how-to-optimize-parallel-computing-parameters

Could you please let me know how to fix this?

Thanks, Daniel

moold commented 1 year ago

I think you can manually run the failed subtasks, and then re-run Nextdenovo.

XXH123a commented 1 year ago

Dear Devs,

I am running NextDenovo (v2.5.0) on a 2.4Gb mammalian genome using Nanopore data in Docker with Ubuntu 20.04.2 LTS and Python 3.10.6 in a Nextflow pipeline (allocated cpus = 16, memory = 286.GB).

The requirements were installed like this in docker:

RUN git clone https://github.com/moold/ParallelTask && cd ParallelTask && git reset --hard ffd4e15afb5f4a450c46b766bb02763d648c187d && pip install .
RUN wget https://github.com/Nextomics/NextDenovo/releases/download/v2.5.0/NextDenovo.tgz --no-check-certificate && tar -vxzf NextDenovo.tgz && cd NextDenovo && cd / && rm NextDenovo.tgz

Soon after "[39 INFO] 2023-02-19 07:55:52 raw_align done", I am getting "returned non-zero exit status 134". Please see the log file here: command.log

If this is a resource issue, I have followed the resource optimization guideline here: https://nextdenovo.readthedocs.io/en/stable/FAQ.html#how-to-optimize-parallel-computing-parameters

Could you please let me know how to fix this?

Thanks, Daniel

Excuse me, I also encountered the same error. How did you solve it?