Muscle Alignment/ ITS sequences

[Lluvia Vargas]

Hi ! +

I am having the following problems while trying t run alighment of ITS sequences with muscle through qiime... I dont know if I am doing something wrong in the command line or if there is something odd with my files, since I ger Error alerts (please see below). I am copying the error lines that pop out after hiting enter in the command line.

Many thanks!

Lluvia




qiime@qiime-VirtualBox:~/Desktop/Shared_Folder/Secuencias_VDP/Sec_VDP$ align_seqs.py -i Analysis/Split_Library_Output/seqs.fna -m muscle -o Analysis/alignment_muscle
Traceback (most recent call last):
  File "/home/qiime/qiime_software/qiime-1.7.0-release/bin/align_seqs.py", line 205, in <module>
    main()
  File "/home/qiime/qiime_software/qiime-1.7.0-release/bin/align_seqs.py", line 202, in main
    log_path=log_path)
  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/align_seqs.py", line 114, in __call__
    log_path=log_path, *args, **kwargs)
  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/util.py", line 277, in __call__
    result = self.getResult(*args, **kwargs)
  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/align_seqs.py", line 108, in getResult
    result = module.align_unaligned_seqs(seqs, moltype=DNA, params=params)
  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/muscle_v38.py", line 554, in align_unaligned_seqs
    res = app(int_map.toFasta())
  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 274, in __call__
    out,err,exit_status,self._get_result_paths(data))
  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 291, in _handle_app_result_build_failure
    raise ApplicationError, "Error constructing CommandLineAppResult."
cogent.app.util.ApplicationError: Error constructing CommandLineAppResult.

[Tony Walters]

Hello Lluvia,

Can you run print_qiime_config.py -t

and verify that muscle is showing as installed?

Also, you might have issues with trying to align ITS sequences, although it may work with a group of very closely related sequences.

-Tony

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