Comments (2)
I think you can manually run the failed subtasks, and then re-run Nextdenovo.
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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?
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Related Issues (20)
- What's the difference between -A and -q 10 in nextgraph_options HOT 12
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- Can you run nextDenovo without a config file? HOT 1
- TypeError: unsupported operand type(s) HOT 2
- long time for assemling genome HOT 6
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- telomeres getting lost HOT 6
- [4501 ERROR] 2023-06-13 22:29:40 the input data is insufficient for an assembly. HOT 3
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