Problem with NextPolish for centos6.9

[misago162]

Hello

I'm trying to use the NextPolish 1.3.1 precompiled for CentOS 6.9, but when I run the tests I receive this error message:

[misanchez@login2 NextPolish]$ ./nextPolish test_data/run.cfg Traceback (most recent call last): File "./nextPolish", line 403, in main(args) File "./nextPolish", line 239, in main from taskControl import Task, Run File "/home/crgadm/misanchez/software-downloaded/NextPolish-Centos-6.9/NextPolish/lib/taskControl.py", line 238 self.drmaa.exit() ^ TabError: inconsistent use of tabs and spaces in indentation [misanchez@login2 NextPolish]$

With the NextDenovo 2.4.0 precompiled for CentOS 6.9 I don't have this problem, it works fine.

Can you help me with this proble? Can I do something to fix this proble.

Operative System:

Red Hat Enterprise Linux Server release 6.7 (Santiago)

GCC:

gcc version 6.3.0 (GCC) Python:

Python 3.8.6

NextPolish release:

NextPolish-CentOS6.9.tgz

To Reproduce:

run the test: /nextPolish test_data/run.cfg

Thanks

Miguel

[moold]

It seems you have changed the code in taskControl.py, so you can download NextPolish again or replace taskControl.py with the one in NextDenovo directory.

[misago162]

Hi moold

I'm sorry but I haven't modify any file, the problem arise just after download and decompress the tgz file:

[misanchez@login1 NextPolish-Centos-6.9]$ mkdir tmp [misanchez@login1 NextPolish-Centos-6.9]$ cd tmp/ [misanchez@login1 tmp]$ wget https://github.com/Nextomics/NextPolish/releases/download/v1.3.1/NextPolish-CentOS6.9.tgz --2021-02-05 10:02:00-- https://github.com/Nextomics/NextPolish/releases/download/v1.3.1/NextPolish-CentOS6.9.tgz Resolving github.com... 140.82.121.3 Connecting to github.com|140.82.121.3|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://github-releases.githubusercontent.com/185516643/74cf9300-27fa-11eb-9c63-24b7f28920c8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210205%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210205T090142Z&X-Amz-Expires=300&X-Amz-Signature=3d778e79ea16b4a9ce582f548c1e942624b12e30962cd9f67dee55da9977df86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=185516643&response-content-disposition=attachment%3B%20filename%3DNextPolish-CentOS6.9.tgz&response-content-type=application%2Foctet-stream [following] --2021-02-05 10:02:00-- https://github-releases.githubusercontent.com/185516643/74cf9300-27fa-11eb-9c63-24b7f28920c8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210205%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210205T090142Z&X-Amz-Expires=300&X-Amz-Signature=3d778e79ea16b4a9ce582f548c1e942624b12e30962cd9f67dee55da9977df86&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=185516643&response-content-disposition=attachment%3B%20filename%3DNextPolish-CentOS6.9.tgz&response-content-type=application%2Foctet-stream Resolving github-releases.githubusercontent.com... 185.199.109.154, 185.199.111.154, 185.199.110.154, ... Connecting to github-releases.githubusercontent.com|185.199.109.154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 17678055 (17M) [application/octet-stream] Saving to: “NextPolish-CentOS6.9.tgz”

100%[======================================================================================================>] 17,678,055 9.08M/s in 1.9s

2021-02-05 10:02:02 (9.08 MB/s) - “NextPolish-CentOS6.9.tgz” saved [17678055/17678055]

[misanchez@login1 tmp]$ tar xzf NextPolish-CentOS6.9.tgz [misanchez@login1 tmp]$ cd NextPolish [misanchez@login1 NextPolish]$ ./nextPolish test_data/run.cfg Traceback (most recent call last): File "./nextPolish", line 511, in main(args) File "./nextPolish", line 339, in main from task_control import Task, Run File "/home/crgadm/misanchez/software-downloaded/NextPolish-Centos-6.9/tmp/NextPolish/lib/task_control.py", line 8, in import psutil ImportError: No module named psutil [misanchez@login1 NextPolish]$

[misago162]

Hi If I download the source package from here:

https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish-CentOS6.9.tgz

I can build it and it works.

It seems the problem is in the precompiled package:

https://github.com/Nextomics/NextPolish/releases/download/v1.3.1/NextPolish-CentOS6.9.tgz

[moold]

Actually, https://github.com/Nextomics/NextPolish/releases/latest/download/NextPolish-CentOS6.9.tgz and https://github.com/Nextomics/NextPolish/releases/download/v1.3.1/NextPolish-CentOS6.9.tgz is the same file.

[moold]

For problems like ImportError: No module named psutil, you need install these modules using pip install psutil

[misago162]

You are right, I forgot to loadl the correct python modulefile, it is the reason of the psutil library problem.

It seems the tgz that I downloaded yesterday is different that the tgz that I downloades this morning:

[misanchez@login1 NextPolish-Centos-6.9]$ ls -l NextPolish-CentOS6.9.tgz -rw-r--r-- 1 misanchez crgadm 17134328 Jul 19 2019 NextPolish-CentOS6.9.tgz [misanchez@login1 NextPolish-Centos-6.9]$ ls -l tmp/NextPolish-CentOS6.9.tgz -rw-r--r-- 1 misanchez crgadm 17678055 Nov 16 03:57 tmp/NextPolish-CentOS6.9.tgz [misanchez@login1 NextPolish-Centos-6.9]$ md5sum tmp/NextPolish-CentOS6.9.tgz 6a520f5a461901d7140e8472ae72a47c tmp/NextPolish-CentOS6.9.tgz [misanchez@login1 NextPolish-Centos-6.9]$ md5sum NextPolish-CentOS6.9.tgz 605ca116b18670ecfaaca40803b6e255 NextPolish-CentOS6.9.tgz [misanchez@login1 NextPolish-Centos-6.9]$

But no worry, it doesn't mind, now it is working, you can close the ticket. Thanks a lot.