Failing with error about MSPminer

[WenjinZhang]

When I run the MetaWIBELE-characterize workflow with demo files, I get an error:

07/08/2024 04:59:44 PM - LoggerReporter - INFO: task 41, mspminer : ready and waiting for resources
(Jul 08 16:59:44) [34/51 -  66.67%] **Ready    ** Task 41: mspminer
07/08/2024 04:59:44 PM - LoggerReporter - INFO: task 41, mspminer : starting to run
(Jul 08 16:59:44) [34/51 -  66.67%] **Started  ** Task 41: mspminer
07/08/2024 04:59:44 PM - LoggerReporter - INFO: Executing with shell:  mspminer /parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/MSPminer_setting.cfg >/parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/metawibele_MSPminer_msp.run_mspminer.log 2>&1
07/08/2024 04:59:50 PM - LoggerReporter - ERROR: task 41, mspminer :  Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
  File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/runners.py", line 200, in _run_task_locally
    action_func(task)
  File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/helpers.py", line 107, in actually_sh
    ret = _sh(s, **kwargs)
  File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/util/__init__.py", line 320, in sh
    raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8')))
anadama2.util.ShellException: [Errno 255] Command `mspminer /parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/MSPminer_setting.cfg >/parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/metawibele_MSPminer_msp.run_mspminer.log 2>&1' failed.
Out:
Err:
(Jul 08 16:59:50) [35/51 -  68.63%] **Failed   ** Task 41: mspminer

I guess it’s a problem with the MSPminer execution. I checked the path my input files, the permissions of the settings.ini, and the path of MSPminer has been added in the .bashrc. Everything seems just fine. I also got some results in the MSPminer_output. The metawibele_MSPminer_msp.run_mspminer.log file also didn’t show any errors.

Plus, I treid to run MSPminer alone without metaWIBELE using the command ./mspminer settings.ini(with demo_genecatalogs_counts.all.refined.tsv as the input file), it seems that there is no error. The output of the command line is as follows

(mw) [zhangwj02@mu02 MSPminer_1_1_3]$ ./mspminer settings.ini
MSPminer - version 1.1.3
(C) Copyright 2016-2023 Enterome & INRAE

Reading count matrix...
Done. Count matrix has 604 genes quantified across 102 samples.

Computing number of mapped reads in samples...
Done.

Computing sqrt transformation of genes counts...
Done.

Filtering too rare genes...
Done. 569 genes remaining.

Creating genes bins...
Done. Genes split in 102 bins.

Creating seeds...
Done. 0 seeds created.

Printing all seeds...
Done.

Merging seeds...
Done. 0 seeds remaining.

Printing merged seeds...
Done.

Extracting core seeds ...
Done. 0 core seeds extracted.

Printing core seeds...
Done.

Creating Metagenomic Species Pan-genomes...
Metagenomic species creation done.

Printing Metagenomic Species Pan-genomes...
Done.

Time Statistics:
Reading count matrix: 0 min 0 sec
Computing number of mapped reads in samples: 0 min 0 sec
Sqrt transformation: 0 min 0 sec
Filtering rare genes: 0 min 0 sec
Creating genes bins: 0 min 0 sec
Creating seeds: 0 min 5 sec
Printing all seeds: 0 min 0 sec
Merging seeds: 0 min 0 sec
Printing merged seeds: 0 min 0 sec
Extracting core seeds: 0 min 0 sec
Printing core seeds: 0 min 0 sec
Creating Metagenomic Species Pan-genomes: 0 min 0 sec
Printing Metagenomic Species Pan-genomes: 0 min 0 sec
Total: 0 min 5 sec

I don’t know what went wrong. Can you please help me with this problem? Thank you very much.

[YancongZhang]

Hi there,

Could you try this command
mspminer /parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/MSPminer_setting.cfg >/parastor/home/zhangwj02/MetaWIBELE/res/abundance_annotation/metawibele_MSPminer_msp.run_mspminer.log 2>&1
and see if it works without errors?

To help me debug, do you mind sharing with me the whole running logs that were printed to the screen when you run MetaWIBELE?

Thanks!
Yancong

[WenjinZhang]

I tried to run this command but nothing happened, I did not get any output.

When I run the MetaWIBELE-characterize workflow, all running logs that printed to the screen are as follows:

This is the content of metawibele_MSPminer_msp.run_mspminer.log file:

Thanks very much Yancong!

[YancongZhang]

Hi there,

It looks like that you mixed the outputs from multiple failed runs. Could you please clear up your output folder, rerun MetaWIBELE-characterize and save the screen logs into a file (e.g. characterize.log)?

If you still see errors, to help me further debug, do you mind sending me your full output folder along with the characterize.log file and the metawibele.cfg file? You can also share these with me via email (yancong@broadinstitute.org) if you prefer to?

Thanks!
Yancong