Qiime Assembly error

Question

[rahul.yadav1906]

I got this error "Command returned exit status: 1" when i was trying to run pick_de_novo_outs.py for qiime analysis. May any one please tell me what error is it and how to fix it?

[rahul.yadav1906]

pick_de_novo_otus.py -i /xxx/xxx/xxx/xx.fna -o /xxx/xxx/xxx/uclust_otus/ -f
Traceback (most recent call last):
  File "/usr/local/bin/pick_de_novo_otus.py", line 180, in <module>
    main()
  File "/usr/local/bin/pick_de_novo_otus.py", line 177, in main
    status_update_callback=status_update_callback)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/upstream.py", line 306, in run_pick_de_novo_otus
    close_logger_on_success=close_logger_on_success)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError: 

*** ERROR RAISED DURING STEP: Pick OTUs
Command run was:
 pick_otus.py -i /xxx/xxx/xxx/xx.fna -o /xxx/xxx/xxx/uclust_otus//uclust_picked_otus 
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/pick_otus.py", line 1004, in <module>
    main()
  File "/usr/local/bin/pick_otus.py", line 792, in main
    result_path=result_path, log_path=log_path, HALT_EXEC=False)
  File "/usr/local/lib/python2.7/dist-packages/qiime/pick_otus.py", line 1286, in __call__
    HALT_EXEC=HALT_EXEC)
  File "/usr/local/lib/python2.7/dist-packages/bfillings/uclust.py", line 595, in get_clusters_from_fasta_filepath
    clusters_from_uc_file(uclust_cluster['ClusterFile'])
  File "/usr/local/lib/python2.7/dist-packages/bfillings/uclust.py", line 301, in clusters_from_uc_file
    raise UclustParseError("Query id " + query_id + " hit multiple seeds. "
bfillings.uclust.UclustParseError: Query id QiimeExactMatch.M01606:67:000000000-BHBJ9:1:1102:23194:5365 hit multiple seeds. This can happen if --allhits is enabled in the call to uclust, which isn't supported by default. Call clusters_from_uc_file(lines, error_on_multiple_hits=False) to allow a query to cluster to multiple seeds.

Answer 1

[h.mon]

Python error messages are already difficult to read, but the lack of formatting from your copy/pasted error makes it even worse.

If you search for This can happen if --allhits is enabled in the call to uclust you will find the most likely cause of the problem and some solutions, e.g. here, here and here.

[rahul.yadav1906]

Thank You for your reply. I will check this. Thank You once again

Answer 2

[rahul.yadav1906]

May please anyone help me with the step by step tutorial guide for QIIME de_novo and reference based assembly.

Thanking You. Rahul Yadav