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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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error on slurm system

zskey-zn opened this issue · comments

commented

Describe the bug
Hi, I run nextdenovo(2.4.0) on slurm sysytem, but it can't work Successfully.I have downloaded these package.

cmd>module load  nextdenovo/2.4.0
Loading nextdenovo/2.4.0
  Loading requirement: python/3.7.10 drmaa/1.1.2

Error message

python3: error: s_p_parse_file: unable to status file /usr/local/etc/slurm.conf: No such file or directory, retrying in 1sec up to 60sec
python3: error: ClusterName needs to be specified
python3: error: Unable to establish controller machine
Traceback (most recent call last):
  File "/public/frasergen/PUB/software/nextdenovo/NextDenovo-2.4.0/nextDenovo", line 856, in 
    main(args)
  File "/public/frasergen/PUB/software/nextdenovo/NextDenovo-2.4.0/nextDenovo", line 598, in main
    task.run.start()
  File "/public/frasergen/PUB/software/nextdenovo/NextDenovo-2.4.0/lib/task_control.py", line 187, in start
    self._sge()
  File "/public/frasergen/PUB/software/nextdenovo/NextDenovo-2.4.0/lib/task_control.py", line 241, in _sge
    jobid = self.drmaa.runJob(jt)
  File "/public/frasergen/PUB/software/python/Python-3.7.10/lib/python3.7/site-packages/drmaa/session.py", line 314, in runJob
    c(drmaa_run_job, jid, sizeof(jid), jobTemplate)
  File "/public/frasergen/PUB/software/python/Python-3.7.10/lib/python3.7/site-packages/drmaa/helpers.py", line 302, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
  File "/public/frasergen/PUB/software/python/Python-3.7.10/lib/python3.7/site-packages/drmaa/errors.py", line 151, in error_check
    raise _ERRORS[code - 1](error_string)
drmaa.errors.InternalException: code 1: slurm_submit_batch_job error (2): No such file or directory

my cfg file

[General]
job_type = slurm
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 2
input_type = raw
read_type = clr
input_fofn = input.fofn
workdir = ./01_rundir
cluster_options =  --cpus-per-task={cpu} --mem-per-cpu={vf}

[correct_option]
read_cutoff = 1k
genome_size = 308161
pa_correction = 2
sort_options = -m 1g -t 2
minimap2_options_raw =  -t 8
correction_options = -p 15

[assemble_option]
minimap2_options_cns =  -t 8
nextgraph_options = -a 1

how to dedug this problem?

commented

I suppose the problem in this.

export SLURM_ROOT=/opt/gridview/slurm
export SLURM_CELL=default

in SGE:
the correct code is

export SGE_ROOT=/opt/sge
export SGE_CELL=default

so, when I run the nextdenovo code in slurm, how to set "root" and "cell" in my code?

commented

Try the latest version, which does not require drmaa.

commented