hmmpfam.pre_overlap_analysis (prok. pipeline)

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hmmpfam.pre_overlap_analysis (prok. pipeline)

Julian Krauskopf
Hello, i have aproblem with the component hmmpfam.pre_overlap_analysis. it fails in the command:

/usr/bin/hmmpfam --acc /usr/local/projects/db/Pfam_ls /usr/local/projects/test/output_repository/translate_sequence/9_translate/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6206.1.fsa

with the error

FATAL 09:15:48:074 [Thread: ID:22961 - hmmpfam] ExceptionHandler handleExceptionQuietMode:137 Runtime error executing command /usr/bin/hmmpfam --acc  /usr/local/projects/db/Pfam_ls /usr/local/projects/test/output_repository/translate_sequence/9_translate/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6226.1.fsa 1> /usr/local/projects/test/output_repository/hmmpfam/9_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6226.1.raw
Error executing script exit value: 1
FATAL: Failed to open HMM database /usr/local/projects/db/Pfam_ls
Usage: hmmpfam [-options]  
  Available options are:
   -h        : help; print brief help on version and usage
   -n        : nucleic acid models/sequence (default protein)
   -A     : sets alignment output limit to  best domain alignments
   -E     : sets E value cutoff (globE) to ; default 10
   -T     : sets T bit threshold (globT) to ; no threshold by default
   -Z     : sets Z (# models) for E-value calculation

When i run the same command through the shell it works.


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