Comments (4)
This is usually caused by the compute nodes and the master node using different Python programs.
Try:
`which python` nextDenovo run.cfg
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Hi developer,
Thank you for helping me on this, now the tool can move forward. But I came across another error reported as [" returned non-zero exit status 134, error info"].
I saw there are 65 jobs in total for raw align step, 59 jobs failed, and the program try to rerun the other failed for three times. I guess the failure is due to the full of RAM and thread, right?
The program is still running, I monitoring its CUP and RAM, CPU is 100% in use and RAM is 80% , I assume most of jobs will still fail after three times attempts, right?
my code is pasted as below, which parameters I can optimize to reduce CPU usage for passing this step? parallel_jobs or minimap2's "-t", I am confused with this two parameters. THank you very much! Looking forward to get assembly from this tool!
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 12
input_type = raw
read_type = ont
input_fofn = ./input.fofn
workdir = ./01_rundir
[correct_option]
read_cutoff = 3k
genome_size = 3100000000
pa_correction = 10
sort_options = -m 300g -t 12 -k 27
minimap2_options_raw = -t 12 -x ava-ont
correction_options = -p 15
[assemble_option]
minimap2_options_cns = -t 12
nextgraph_options = -a 1
from nextdenovo.
The computer RAM is not enough, see here to optimize parallel computing parameters.
from nextdenovo.
If you still have problems you should open a new issue where the problem in this issue has already been solved.
from nextdenovo.
Related Issues (20)
- sort_align step erro HOT 1
- Does NEXTDENOVO filter the contig before output? HOT 2
- Error: db_stat failed ? HOT 1
- ERROR:the input data is insufficient for an assembly HOT 3
- Question about error rate for correction HOT 1
- ctg_align failed HOT 4
- When run nextdenovo with test_data failed HOT 1
- hello , i used the nextdenovo to assemble the ultra large size genome of 23g, the fq only 270g, just want to assemble the grapgh HOT 7
- How to improve the N50 and reduce contigs numbers? HOT 7
- Test won't run HOT 1
- For low base quality of sequences HOT 1
- Timing out on minimap-nd tasks HOT 4
- I want to correct ONT with HiFi data HOT 1
- db_stat failed, @d84e39c8-130c-4159-bfa9-5393ad703a1a does not exist! HOT 2
- assembly problem HOT 2
- ctg_graph error, (core dumped), returned non-zero exit status 134".
- NextDeNovo running for >4days with no expected outputs HOT 22
- Running out of disk space HOT 3
- Accepted a killed signal and killing all running jobs, please wait...
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