Alpha_rarefaction problem at the collate steps

[Émilie Tremblay]

Hi, I am encountering issues when performing alpha_rarefaction on my samples.

Honestly I do not get what the error message means..

May someone help me here please?

Thanks

python "${qiimePath}"/alpha_rarefaction.py \

>       -i "${Om_merged_biom}"/Om_merged.biom \

>       -m "${analysisFolder}"/Om.meta.tsv \

>       --output_dir "${rarefy_QIIME}"/"Om"/ \

>       -f \

>       -a \

>       -e 100153 \

>       --min_rare_depth 1000 \

>       -n 10 \

>       -O 24

Traceback (most recent call last):

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/bin/alpha_rarefaction.py", line 151, in <module>

    main()

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/bin/alpha_rarefaction.py", line 148, in main

    status_update_callback=status_update_callback)

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/lib/qiime/workflow/downstream.py", line 445, in run_alpha_rarefaction

    close_logger_on_success=close_logger_on_success)

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/lib/qiime/workflow/util.py", line 117, in call_commands_serially

    raise WorkflowError, msg

qiime.workflow.util.WorkflowError: 

*** ERROR RAISED DURING STEP: Collate alpha

Command run was:

 /isilon/biodiversity/pipelines/qiime-1.7.0/python-2.7.3-release/bin/python /isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/bin/collate_alpha.py -i /home/CFIA-ACIA/tremblaye/NGS_for_Fungi_Detection/dataAn/raref_QIIME/Om//alpha_div/ -o /home/CFIA-ACIA/tremblaye/NGS_for_Fungi_Detection/dataAn/raref_QIIME/Om//alpha_div_collated/ 

Command returned exit status: 1

Stdout:

Stderr

Traceback (most recent call last):

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/bin/collate_alpha.py", line 125, in <module>

    main()

  File "/isilon/biodiversity/pipelines/qiime-1.7.0/qiime-1.7.0-release/bin/collate_alpha.py", line 109, in main

    for metric in all_metrics:

TypeError: 'NoneType' object is not iterable

[TonyWalters]

Hello Emily,

You're a few versions back in QIIME, but, I'm guessing that the problem is that you're using the PD_whole_tree metric with a very limited/problematic tree (the ITS region does not lend itself to building trees).

I would specify a parameters file and (sands the PD_whole_tree metric) with alpha_diversity.py, as listed in this thread, and pass with the -p parameter when calling alpha_rarefaction.py:
https://groups.google.com/forum/#!topic/qiime-forum/bhJB-VIIa-0/discussion

[Émilie Tremblay]

Ok. Thanks