[Bio-linux-dev] qiime workflow errors

[Martin Ostrowski]

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?