Question: Problem in QIIME: Cannot run OTU picking script.
0
gravatar for adhirajnath14
4 months ago by
adhirajnath1430 wrote:

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?

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by adhirajnath1430

Are you missing a commandline option that corresponds to the number of jobs to start? The error is essentially complaining that there is no value in the variable default_jobs_to_start. This may be a bug in the code (an unset default or something), but QIIME is pretty mature at this point so something more cryptic is probably happening.

ADD REPLYlink written 4 months ago by Joe16k

I am not sure if I'm missing anything. I have seen people following the same protocol and get the analysis done.

ADD REPLYlink written 4 months ago by adhirajnath1430

From the docs:

-O, --jobs_to_start
Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 1]

There should be a default for this, so it might not be the case, but try re-running your command and specify -O explicity. Long shot, but you weren't by any chance confusing/typo-ing -O and -o?

ADD REPLYlink written 4 months ago by Joe16k

First of all qiime 1.9 it's an outdated version and it's legacy code. But if you want to analize you data with qiime 1.9 using the open approach you need the -r option with the path to the greengenes/silva fasta file, otherwise you will get an error.

And if you want also, you need to define the parameters of the picking method with the -p option

ADD REPLYlink written 3 months ago by zorbax130
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