Problem in QIIME: Cannot run OTU picking script.

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Adhiraj Nath

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Jan 6, 2020, 1:32:02 PM1/6/20
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I am working with metagenomic data where I have already joined the forward & reverse pairs and converted them to .fna format using QIIME scripts. As the next step is to pick OTUs, I'm trying to execute:


pick_open_reference_otus.py -i input.fna -o otu_out/
 


However while running the script, it produces the following error:



Traceback (most recent call last):
  File "/home/ubora/.local/bin/pick_open_reference_otus.py", line 453, in <module>
    main()
  File "/home/ubora/.local/bin/pick_open_reference_otus.py", line 394, in main
    default_jobs_to_start, parallel, option_parser)
  File "/home/ubora/.local/lib/python2.7/site-packages/qiime/workflow/util.py", line 160, in validate_and_set_jobs_to_start
    if (jobs_to_start != int(default_jobs_to_start)) and \
TypeError: int() argument must be a string or a number, not 'NoneType'

I ran the QIIME configuration test to check if there was any problem with the installation.

QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.031s
OK

 

But it seems there's no issue with the installation. Can anyone please help me solve this problem?

TonyWalters

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Jan 6, 2020, 1:42:36 PM1/6/20
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Hello,

I'm going to start with a general statement about QIIME 1-it's not being updated any more, and unless there is a specific reason you need to use QIIME 1 (e.g. replicate a specific analysis), I'd strongly recommend moving to QIIME 2: https://qiime2.org/

That being said, it sounds like you're .qiime_config file (should be the filepath $HOME/.qiime_config) has an invalid parameter. You can make a backup copy of this file and then modify it, or test it with:
print_qiime_config.py
and see if it shows an error or strange setting for the parallel jobs, which looks like it is causing the error above.

-Tony

Adhiraj Nath

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Jan 6, 2020, 2:10:35 PM1/6/20
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my qiime_config file looks like this:

cat $HOME/.qiime_config
assign_taxonomy_id_to_taxonomy_fp
assign_taxonomy_reference_seqs_fp
blastmat_dir
blastall_fp
cluster_jobs_fp
denoiser_min_per_core
jobs_to_start
pick_otus_reference_seqs_fp
pynast_template_alignment_blastdb
pynast_template_alignment_fp
sc_queue
seconds_to_sleep
slurm_memory
slurm_queue
temp_dir
topiaryexplorer_project_dir
torque_queue
slurm_time

I'm not sure. Does anything look wrong here?

TonyWalters

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Jan 6, 2020, 2:24:19 PM1/6/20
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well it looks like there isn't anything set-you might just rename that file to bak_qiime_config and let it run with the defaults.

Adhiraj Nath

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Jan 6, 2020, 2:33:27 PM1/6/20
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I removed the line jobs_to_start. Now it's working fine.

Thanks for your help

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