[Bio-linux-dev] qiime workflow errors

[Tim Booth]

Hi Martin,

Thanks for the bug report.  The trick with these big errors is to start
reading at the end - the last line says Python tried to read a file and
couldn't find it, but it doesn't say explicitly which file.  The error
happened while running a subcommand
(/usr/lib/qiime/bin//beta_diversity.py).  The stack trace is from the
outer command so it's not much use, but Qiime does tell you exactly how
the subcommand was invoked (just under "Command run was:"), so can you
try running it directly?  Do you get the same message?

I did a grep on the file /usr/lib/qiime/bin//beta_diversity.py and this
exact error message only appears once, when the script can't open
opts.input_path, which I think is the file specified by the -i
parameter, ie. "counts_by_group_syn_forqiime.txt".  Are you sure the
file name is spelled correctly?  Is it in the current working directory?

Cheers,

TIM

On Mon, 2011-04-04 at 15:34 +0100, Martin Ostrowski wrote:
> I am stumped at the bottom of the python learning curve with qiime
> 
> see below the error upon entering my jackknifed_beta_diversity.py command. There is an extra backslash before the beta_diversity.py command. I am not sure how to get rid of it.
> 
> Thanks for any advice
> 
> 
> mostrowski at phyto[qiime]  qiime > jackknifed_beta_diversity.py -i counts_by_group_syn_forqiime.txt -t NJ2.tree -o wf_jack -e 5 -v -m mapping_file_v1.txt -p  qiime_parameters.txt
> Beta Diversity (weighted_unifrac, unweighted_unifrac)
> python /usr/lib/qiime/bin//beta_diversity.py -i counts_by_group_syn_forqiime.txt -o wf_jack --metrics weighted_unifrac,unweighted_unifrac -t NJ2.tree
> Traceback (most recent call last):
>   File "/usr/lib/qiime/bin/jackknifed_beta_diversity.py", line 150, in <module>
>     main()
>   File "/usr/lib/qiime/bin/jackknifed_beta_diversity.py", line 146, in main
>     master_tree=master_tree)
>   File "/usr/lib/python2.6/dist-packages/qiime/workflow.py", line 1086, in run_jackknifed_beta_diversity
>     command_handler(commands,status_update_callback,logger)
>   File "/usr/lib/python2.6/dist-packages/qiime/workflow.py", line 130, in call_commands_serially
>     raise WorkflowError, msg
> qiime.workflow.WorkflowError: 
> 
> *** ERROR RAISED DURING STEP: Beta Diversity (weighted_unifrac, unweighted_unifrac)
> Command run was:
>  python /usr/lib/qiime/bin//beta_diversity.py -i counts_by_group_syn_forqiime.txt -o wf_jack --metrics weighted_unifrac,unweighted_unifrac -t NJ2.tree
> Command returned exit status: 1
> Stdout:
> 
> Stderr
> io error, input path not valid.  Does it exist?
> 
> 
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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
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Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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