hmmpfam.pre_overlap_analysis (prok. pipeline)

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hmmpfam.pre_overlap_analysis (prok. pipeline)

Julian Krauskopf
i passed this error by changing some permissions but now i get another one within this component.

/opt/ergatis/bin/hmmpfam2htab --donotrun=0 --input_file=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.raw --output_htab=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.htab --mldbm_file='$;HMM_LIB_DB$;'

MLDBM error: Second level tie failed, "No such file or directory" at /opt/ergatis/bin/hmmpfam2htab.pl line 191
Unable to tie hash to $;HMM_LIB_DB$; at /opt/ergatis/bin/hmmpfam2htab.pl line 191

the HMM_LIB_DB is set in software.config and points to the databaselibrary for hmmer

thanks
julian
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Re: hmmpfam.pre_overlap_analysis (prok. pipeline)

Chris Hemmerich

Julian,

  Our dev environment has been down all day for electrical work so I
haven't been able to try to reproduce this.

The HMM_LIB_DB variable should have been replaced with the value in
software.config. The simplest cause would be a problem in software.config
- double check that HMM_LIB_DB is typed correctly and exists in the
[common inputs] section.

After that, the next step is to check the config file for the component
(either by clicking on the config button in the web view, or checking the
final.config file in the runtime directory for the component. Make sure
that the [common inputs] section show up there and that HMM_LIB_DB is
correct.

  Chris


On Tue, 21 Sep 2010, Julian Krauskopf wrote:

> i passed this error by changing some permissions but now i get another one within this component.
>
> /opt/ergatis/bin/hmmpfam2htab --donotrun=0
> --input_file=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.raw
> --output_htab=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.htab
> --mldbm_file='$;HMM_LIB_DB$;'
>
> MLDBM error: Second level tie failed, "No such file or directory" at /opt/ergatis/bin/hmmpfam2htab.pl line 191
> Unable to tie hash to $;HMM_LIB_DB$; at /opt/ergatis/bin/hmmpfam2htab.pl line 191
>
> the HMM_LIB_DB is set in software.config and points to the databaselibrary for hmmer
>
> thanks
> julian
> --
> GRATIS: Spider-Man 1-3 sowie 300 weitere Videos!
> Jetzt freischalten! http://portal.gmx.net/de/go/maxdome
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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> Ergatis-users mailing list
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>

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Re: hmmpfam.pre_overlap_analysis (prok. pipeline)

Julian Krauskopf
In reply to this post by Julian Krauskopf
even if i put the path in the command i get the same error

/opt/ergatis/bin/hmmpfam2htab --donotrun=0
--input_file=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.raw
--output_htab=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.htab
--mldbm_file=/usr/local/projects/db/Pfam_ls


MLDBM error: Second level tie failed, "No such file or directory" at /opt/ergatis/bin/hmmpfam2htab.pl line 191
Unable to tie hash to /usr/local/projects/db/Pfam_ls at /opt/ergatis/bin/hmmpfam2htab.pl line 191.

what is the mldbm_file? in my config it points to the same lib then hmm_all and hmm_info

Greetings
Julian
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Re: hmmpfam.pre_overlap_analysis (prok. pipeline)

Aaron Buechlein
Hi Julian,
Chris has asked me to respond regarding your error.  First, we don't
actually run hmmpfam2htab.  In the config  file for hmmpfam, we set
$;SKIP_HTAB$; = 1.  That will set the --donotrun flag = 1 and will allow
you to skip that portion of the process.  Now, I can try to explain how
I created our hmm library.  Our coding_hmm.lib is just the concatenation
of Pfam-A.hmm and TIGRFAMs_9.0_HMM.LIB (or whatever is the latest
release).  I simply download them and then cat them together.  Next, if
you check out ergatis from svn, you will see a util directory.  Within
that directory are some scripts that create the mldbm file from your hmm
library, namely hmmlib_to_mldbm.pl, go_mapping_file_to_mldbm.pl, and
tigrfam_info_to_mldbm.pl.  I'm not going to go into detail into how to
run those scripts as they have pretty good documentation in them.  Below
is my workflow for generating our hmm libraries.  Hope this helps.

    cat Pfam\-A.hmm TIGRFAMs_9.0_HMM.LIB > coding_hmm.lib
    download http://www.geneontology.org/external2go/tigrfams2go
    download http://www.geneontology.org/external2go/pfam2go
    run util script hmmlib_to_mldbm.pl to make mldbm.db file
    run util script go_mapping_file_to_mldbm.pl to add tigrfams2go and
    pfam2go info to mldbm.db
    download ftp://ftp.jcvi.org/pub/data/TIGRFAMs/TIGRFAMs_9.0_INFO.tar.gz
    run util script tigrfam_info_to_mldbm.pl to add TIGRFAMS_INFO to
    mldbm.db
    hmmconvert -b coding_hmm.lib coding_hmm.lib.bin

Thanks,

Aaron Buechlein

Julian Krauskopf wrote:

> even if i put the path in the command i get the same error
>
> /opt/ergatis/bin/hmmpfam2htab --donotrun=0
> --input_file=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.raw
> --output_htab=/usr/local/projects/test/output_repository/hmmpfam/10_pre_overlap_analysis/i1/g1/gi_169235049_ref_NC_010364.polypeptide.6456.1.htab
> --mldbm_file=/usr/local/projects/db/Pfam_ls
>
>
> MLDBM error: Second level tie failed, "No such file or directory" at /opt/ergatis/bin/hmmpfam2htab.pl line 191
> Unable to tie hash to /usr/local/projects/db/Pfam_ls at /opt/ergatis/bin/hmmpfam2htab.pl line 191.
>
> what is the mldbm_file? in my config it points to the same lib then hmm_all and hmm_info
>
> Greetings
> Julian
>  

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