ImportError

[mergi-2674]

Describe the bug
I was trying to run NextPolish on a cluster on six nodes each with 128GB of RAM. I installed according to the instruction explained on the read the io page. However, it always gives me an error that says,

Error message
Traceback (most recent call last):
File "/home/users/piwczyn/miniconda3/envs/nextpolish/NextPolish/nextPolish", line 11, in
from paralleltask import Task
ImportError: No module named "paralleltask",

even if the module is there.
I was using a cluster with

Operating system
Which operating system and version are you using?
redhat-linux-x86_64

GCC
What version of GCC are you using?
gcc version 4.8.5

Python
What version of Python are you using?
Python 3.9.12

NextPolish
What version of NextPolish are you using?
NextPolish version 1.4.1

Thanks!

[Hu Jiang]

Hello, this is usually caused by using different Pythons between the main and computer nodes. To fix this problem, just use the absolute path of python, try like this /path_to_python/python nextPolish input.cfg

[mergi-2674]

Hi Hu Jiang, Thank you so much for the fastest reply to my email. It works for me the way you suggested. But it fails with this error. Actually, I wanted to run on 4 nodes. Each node has 48 threads and 128 GB of RAM. Here is my configuration file. Is that right? [General] job_type = pbs job_prefix = Ferula_nextPolish_flye task = default rewrite = no deltmp = yes rerun = 3 parallel_jobs = 48 genome = /STORAGE/DATA/xxxxx/assembly.fasta genome_size = auto workdir = /STORAGE/DATA/xxxxxx/01_rundir polish_options = -p {multithread_jobs} [sgs_option] sgs_fofn = /STORAGE/DATA/xxxxxx/sgs.fofn sgs_options = -max_depth 100 [lgs_option] lgs_fofn = /STORAGE/DATA/xxxxxx/lgs.fofn lgs_options = -min_read_len 1k -max_depth 100 lgs_minimap2_options = -x map-ont and the command line script, #!/bin/bash #PBS -N Nextpolish #PBS -M ***@***.*** #PBS -m abe #PBS -l nodes=4:ppn=48 #PBS -l mem=128gb #PBS -l walltime=3500:00:00 #PBS -o /STORAGE/DATA/xxxx/xxxxx/stdout_${PBS_JOBID} #PBS -e /STORAGE/DATA/xxxx/xxxxx/stderr_${PBS_JOBID} Cd /STORAGE/DATA/xxxxxxx /home/users/xxxxxxx/miniconda3/envs/nextpolish/bin/python2.7 /home/users/xxxxxxxx/miniconda3/envs/nextpolish/NextPolish/nextPolish /STORAGE/DATA/xxxxxx/nextpolish.cfg Best, Mergi Dinka E - Mail:- ***@***.*** ***@***.***

…

On Fri, Jul 29, 2022 at 11:43 AM Hu Jiang ***@***.***> wrote: Hello, this is usually caused by using different Pythons between the main and computer nodes. To fix this problem, just use the absolute path of python, try like this /path_to_python/python nextPolish input.cfg — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APX3PXUXLYFYTHFAUX6HQP3VWORU7ANCNFSM55AD6IOQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Hu Jiang]

It's better to set it like this:

parallel_jobs = 4
multithread_jobs = 48

see here for Parameter introduction.

[mergi-2674]

Awesome, thanks! Mergi Dinka E - Mail:- ***@***.*** ***@***.***

…

On Mon, Aug 1, 2022 at 7:43 AM Hu Jiang ***@***.***> wrote: Closed #97 <#97> as completed. — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APX3PXV3MDHLIIJQF6UQZW3VW5PWLANCNFSM55AD6IOQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>