error with make_rarefaction_plots.py

[m. salomez]

Deal all,

I am trying to run the command make_rarefaction_plots.py on Bash integrated in Windows 10. Here the result :

-----------------------------------------------------------------------------------------------
(qiime1) msalomez@LAPTOP-V4QS72OF:~/QiimeMelanie/Analysis16S/AlphaDiv$ alpha_rarefaction.py -i otu_table_mc2_filter.biom -o alphadivfilterbis/ -t rep_set.tre -m mapping_files_corr_falsemid.txt -e 4800
Traceback (most recent call last):
  File "/home/msalomez/miniconda3/envs/qiime1/bin/alpha_rarefaction.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'alpha_rarefaction.py')
  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script

  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script

  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/alpha_rarefaction.py", line 161, in <module>
    main()
  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/alpha_rarefaction.py", line 158, in main
    retain_intermediate_files=retain_intermediate_files)
  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/downstream.py", line 342, in run_alpha_rarefaction
    close_logger_on_success=close_logger_on_success)
  File "/home/msalomez/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Rarefaction plot: All metrics
Command run was:
 make_rarefaction_plots.py -i alphadivfilterbis//alpha_div_collated/ -m mapping_files_corr_falsemid.txt -o alphadivfilterbis//alpha_rarefaction_plots/
Command returned exit status: 134
Stdout:

Stderr
OMP: Error #100: Fatal system error detected.
OMP: System error #22: Invalid argument
Aborted (core dumped)
-------------------------------------------------------------------------------------------------------

I don't understand where this error come from. I have checked the otu table and the mapping file and they seem fine.. I can say also that I did the same operation months ago on an other computer with Xubuntu and it was working well. Does it come from Bash?

Any ideas?

Thank you for your help!!

Melanie

[Colin Brislawn]

Hello Melanie,

You mentioned:

Bash integrated in Windows 10

Can you tell me more about this setup? Are you making use of the new WSL (Windows Subsystem for Linux)?

https://msdn.microsoft.com/en-us/commandline/wsl/about 

While Qiime 1.9.1 has been used well on many flavors of Linux, including Ubuntu, I'm not sure if WSL is currently supported. Also, qiime makes use of many other pieces of software, like uclust, which were compiled for Linux and may not run on WSL.

Thanks for telling me more about your setup.

Colin

[m. salomez]

Hello Colin

Yes, it is indeed Bash/WSL the windows subsystem for linux.

Since now, Qiime was working very well on Bash but I did not use any complex command requiring other software like OTUs picking command.

Melanie

[m. salomez]

Hello Colin,

I did a normal installation of linux and the command is working now. So yes it is coming from using Qiime with Bash.

Thank you for your help

Melanie

[Colin Brislawn]

Thanks for the updates, Melanie.

While I use linux and osx for most bioinformatics, all of my personal machines run Windows. I've been hoping to use WSL to make some standard programs work well on my Windows machines (things like git, gzip, grep, sed).

Because the core of qiime is python, all those native commands should work, but I'm not sure if the qiime devs are interested in getting in running on WSL. I would love to be able to run a quick 'biom summarize' from a Windows machine, but I'm not sure if that day is close.

Thanks for telling me more about WSL. Let me know what else you find,

Colin