train_for_glimmer3_iteration

classic Classic list List threaded Threaded
11 messages Options
Reply | Threaded
Open this post in threaded view
|

train_for_glimmer3_iteration

Julian Krauskopf
Hello,
i have a problem with the 'train for glimmer3' component within the Prokaryotic Annotation Pipeline. The Pipeline works until glimmer3 finished and the train component starts. Then it says :

Software error:

Ran out of memory for input buffer at /usr/lib/perl5/XML/Parser/Expat.pm line 469.
 at /var/www/html/ergatis/cgi/component_summary.cgi line 78

I figured out that this error shows up because the
 
/workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer/component.xml

is empty

and the
/workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer$ cat replace_template_keys.stderr

contains:

Died with 'Bad key $;NFS_TMP_DIR$; in template file' at /opt/ergatis/bin/replace_template_keys.pl line 281

I dont know where the NFS_TMP_DIR is set and why the xml file is empty.

Thanks for any suggestions
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.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Kevin Galens
Julian,

Not sure where the NFS_TMP_DIR came from (it's not in the current subversion
repository). But what this error is telling you is that there is a variable
($;NFS_TMP_DIR$;) in the template file
(/opt/ergatis/docs/trains_for_glimmer3_iteration.xml) which ergatis doesn't
know how to do anything with. Normally, these variables are defined in the
config file. Since the config file is defined as part of the pipeline
template, it doesn't contain the variable $;NFS_TMP_DIR$;.

Is there anyway that the train_for_glimmer3_iteration.xml file was editted?
I can't seem to find an evidence of $;NFS_TMP_DIR$; in subversion.

Kevin


On 9/15/10 9:46 AM, "Julian Krauskopf" <[hidden email]> wrote:

> Hello,
> i have a problem with the 'train for glimmer3' component within the
> Prokaryotic Annotation Pipeline. The Pipeline works until glimmer3 finished
> and the train component starts. Then it says :
>
> Software error:
>
> Ran out of memory for input buffer at /usr/lib/perl5/XML/Parser/Expat.pm line
> 469.
>  at /var/www/html/ergatis/cgi/component_summary.cgi line 78
>
> I figured out that this error shows up because the
>  
> /workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer/component.
> xml
>
> is empty
>
> and the
> /workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer$ cat
> replace_template_keys.stderr
>
> contains:
>
> Died with 'Bad key $;NFS_TMP_DIR$; in template file' at
> /opt/ergatis/bin/replace_template_keys.pl line 281
>
> I dont know where the NFS_TMP_DIR is set and why the xml file is empty.
>
> Thanks for any suggestions
> Julian



------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Chris Hemmerich
In reply to this post by Julian Krauskopf

Hi Julian,

This is a problem introduced by ISGA. We have an underpowered NFS server
at our local site, so we've moved tmp files to local disk rather than NFS.
We've also modified train_for_glimmer3_iteration to be executed over SGE
rather than on the machine where Ergatis is stalled. This causes a problem
because the workflow command that creates the tmp dir generally ends up on
a different node than the workflow command that uses the tmp dir.

The fix is to either

  a) modify project.config to include $;NFS_TMP_DIR$;=

or

  b) modify train_for_glimmer3.iteration.xml to use $;TMP_DIR$; rather than
$;NFS_TMP_DIR$;

If you have TMP_DIR on NFS, option b would be cleaner.

I'll update the ISGA docs and distribution to fix this for the
downloadable version.

Cheers,

Chris

On Wed, 15 Sep 2010, Julian Krauskopf wrote:

> Hello,
> i have a problem with the 'train for glimmer3' component within the Prokaryotic Annotation Pipeline. The Pipeline works until glimmer3 finished and the train component starts. Then it says :
>
> Software error:
>
> Ran out of memory for input buffer at /usr/lib/perl5/XML/Parser/Expat.pm line 469.
> at /var/www/html/ergatis/cgi/component_summary.cgi line 78
>
> I figured out that this error shows up because the
>
> /workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer/component.xml
>
> is empty
>
> and the
> /workflow/runtime/train_for_glimmer3_iteration/38_train_for_glimmer$ cat replace_template_keys.stderr
>
> contains:
>
> Died with 'Bad key $;NFS_TMP_DIR$; in template file' at /opt/ergatis/bin/replace_template_keys.pl line 281
>
> I dont know where the NFS_TMP_DIR is set and why the xml file is empty.
>
> Thanks for any suggestions
> 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.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Julian Krauskopf
In reply to this post by Julian Krauskopf
i dont think that the train_for_glimmer3_iteration.xml file was editted. i guess this file is correkt, or is there something missing?


train_for_glimmer3_iteration.xml

<?xml version="1.0" encoding="UTF-8"?>

<commandSetRoot xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation='commandSet.xsd'>
    <commandSet type="serial">
        <state>incomplete</state>
        <name>train_for_glimmer3 workflow</name>
        <!--Preprocessing-->
        <command>
            <type>RunUnixCommand</type>
            <name>create output directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;OUTPUT_DIRECTORY$;</arg>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>create temp directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;NFS_TMP_DIR$;</arg>
        </command>
        <command>
            <type>RunDistributedCommand</type>
            <name>train for glimmer3 iteration</name>
            <state>incomplete</state>
            <executable>$;BIN_DIR$;/train_for_glimmer3_iteration</executable>
            <param>
                <key>--input_predict_list</key>
                <value>$;INPUT_PREDICT_LIST$;</value>
            </param>
            <param>
                <key>--input_fasta_list</key>
                <value>$;INPUT_FASTA_LIST$;</value>
            </param>
            <param>
                <key>--output_pwm</key>
                <value>$;OUTPUT_PWM$;</value>
            </param>
            <param>
                <key>--tmp_dir</key>
                <value>$;NFS_TMP_DIR$;</value>
            </param>
            <param>
                <key>--glimmer3_dir</key>
                <value>$;GLIMMER3_DIR$;</value>
            </param>
            <param>
                <key>--elph_bin</key>
                <value>$;ELPH_BIN$;</value>
            </param>
            <param>
                <key>--conf_ini_file</key>
                <value>$;REPOSITORY_ROOT$;/workflow/runtime/glimmer3/$;PIPELINEID$;_$;GLIMMER3_OUTPUT_TOKEN$;/glimmer3.$;GLIMMER3_OUTPUT_TOKEN$;.user.config</value>
            </param>      
        </command>
    </commandSet>
</commandSetRoot>


 train_for_glimmer3_iteration.config

[interface]
classification = utility

[parameters]
;; output position weight matrix (used as input to the -b option to glimmer3)
;;[REQUIRED]
$;OUTPUT_PWM$; =
;; output token for glimmer3 (second iteration)
;;[REQUIRED]
$;GLIMMER3_OUTPUT_TOKEN$;=default

[input]
$;INPUT_PREDICT_LIST$; =
$;INPUT_FASTA_LIST$; =

[output]
$;OUTPUT_TOKEN$; = default
$;OUTPUT_DIRECTORY$; = $;REPOSITORY_ROOT$;/output_repository/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;

[component]
$;COMPONENT_NAME$; = train_for_glimmer3_iteration
$;DESCRIPTION$; = none
$;WORKFLOW_REPOSITORY$; = $;REPOSITORY_ROOT$;/workflow/runtime/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
$;PIPELINE_TOKEN$; = unnamed

;The version,revision,tag here is set by an interpolated CVS tag
$;VERSION$; = 2.0
$;RELEASE_TAG$; = $Name$
$;REVISION$;            = $Revision: 5801 $

$;TEMPLATE_XML$; = $;DOCS_DIR$;/$;COMPONENT_NAME$;.xml
$;ITERATOR1$; = i1
$;ITERATOR1_XML$; = $;DOCS_DIR$;/$;COMPONENT_NAME$;.$;ITERATOR1$;.xml

;Distributed options
$;GROUP_COUNT$; = 150
$;NODISTRIB$; = 0

;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =

[include]
$;PROJECT_CONFIG$;=
--
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.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Julian Krauskopf
In reply to this post by Julian Krauskopf
ok, that explains it.
thank you

best regards
Julian

Hi Julian,

This is a problem introduced by ISGA. We have an underpowered NFS server
at our local site, so we've moved tmp files to local disk rather than NFS.
We've also modified train_for_glimmer3_iteration to be executed over SGE
rather than on the machine where Ergatis is stalled. This causes a problem
because the workflow command that creates the tmp dir generally ends up on
a different node than the workflow command that uses the tmp dir.

The fix is to either

  a) modify project.config to include $;NFS_TMP_DIR$;=

or

  b) modify train_for_glimmer3.iteration.xml to use $;TMP_DIR$; rather than
$;NFS_TMP_DIR$;

If you have TMP_DIR on NFS, option b would be cleaner.

I'll update the ISGA docs and distribution to fix this for the
downloadable version.

Cheers,

Chris

--
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!  
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Julian Krauskopf
In reply to this post by Julian Krauskopf
fix b doesnt work, gives me the same error.
but after changing the project.config file it goes on to the next error within train_for_glimmer3.

The failing command is:
/opt/ergatis/bin/train_for_glimmer3_iteration --input_predict_list=/usr/local/projects/test/output_repository/glimmer3/49_iter1/glimmer3.raw.list --input_fasta_list=/usr/local/projects/test/output_repository/split_multifasta/49_default/split_multifasta.fsa.list --output_pwm=/usr/local/projects/test/output_repository/train_for_glimmer3_iteration/49_train_for_glimmer/all.motif --tmp_dir=/usr/local/scratch/new/train_for_glimmer3_iteration/49_train_for_glimmer --glimmer3_dir=/opt/glimmer3 --elph_bin=/opt/ELPH/sources/elph --conf_ini_file=/usr/local/projects/test/workflow/runtime/glimmer3/49_iter2/glimmer3.iter2.user.config

under the error it says :
return value: 0
message: Config error, /working/0could not be created


the stdout and stderr is empty. and when i run this command in the shell it works. i also changed the permissions of the script to www-data, but it still fails

Julian
--
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!  
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Chris Hemmerich

Julian,

I'm not certain, but that looks like maybe a problem with Workflow or
SGE/Condor. Do you have Ergatis and Workflow setup to run jobs on a DCE?

One quick test to help isolate the problem is to paste the failing command
into the shell and run it. If that runs ok, the error is likely in trying
to distribute the command. If it fails, it may give a more informative
error message.

Chris


On Wed, 15 Sep 2010, Julian Krauskopf wrote:

> fix b doesnt work, gives me the same error.
> but after changing the project.config file it goes on to the next error within train_for_glimmer3.
>
> The failing command is:
> /opt/ergatis/bin/train_for_glimmer3_iteration --input_predict_list=/usr/local/projects/test/output_repository/glimmer3/49_iter1/glimmer3.raw.list --input_fasta_list=/usr/local/projects/test/output_repository/split_multifasta/49_default/split_multifasta.fsa.list --output_pwm=/usr/local/projects/test/output_repository/train_for_glimmer3_iteration/49_train_for_glimmer/all.motif --tmp_dir=/usr/local/scratch/new/train_for_glimmer3_iteration/49_train_for_glimmer --glimmer3_dir=/opt/glimmer3 --elph_bin=/opt/ELPH/sources/elph --conf_ini_file=/usr/local/projects/test/workflow/runtime/glimmer3/49_iter2/glimmer3.iter2.user.config
>
> under the error it says :
> return value: 0
> message: Config error, /working/0could not be created
>
>
> the stdout and stderr is empty. and when i run this command in the shell it works. i also changed the permissions of the script to www-data, but it still fails
>
> Julian
> --
> Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
> Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Julian Krauskopf
In reply to this post by Julian Krauskopf
The jobs are running local without an installed DCE
I allready pasted this command into the shell and it works. so the command must be correct.

Now i get this error on pipeline.xml.run.out:


 17:56:04:612 [Thread: ID:10647 - train for glimmer3 iteration] SGEMockServer submit:363  Couldn't create directory needed by server /working/0
WARN 17:56:04:613 [Thread: ID:10647 - train for glimmer3 iteration] CommandProcessor executeCommand:201 Caught Exception for
FATAL 17:56:04:639 [Thread: ID:10647 - train for glimmer3 iteration] ExceptionHandler handleExceptionQuietMode:137 Config error, /working/0could not be created

java.io.IOException: Config error, /working/0could not be created
        at org.tigr.htc.request.SGEMockServer.submit(SGEMockServer.java:366)
        at org.tigr.htc.request.HTCRequest.submit(HTCRequest.java:209)
        at org.tigr.workflow.common.DistributedProcessor.submitHTCRequest(DistributedProcessor.java:258)
        at org.tigr.workflow.common.DistributedProcessor.process(DistributedProcessor.java:147)
        at org.tigr.workflow.common.CommandProcessor.executeCommand(CommandProcessor.java:167)
        at org.tigr.workflow.common.CommandProcessor.run(CommandProcessor.java:271)
        at org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:243)
        at org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:222)
        at org.tigr.antware.shared.concurrent.ThreadPoolWorker.access$000(ThreadPoolWorker.java:26)
        at org.tigr.antware.shared.concurrent.ThreadPoolWorker$1.run(ThreadPoolWorker.java:102)
        at java.lang.Thread.run(Thread.java:619)
Config error, /working/0could not be created


Julian
--
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!  
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Mahurkar, Anup
Workflow needs a working directory to write to which is configured during install. I this case it appears to be /working. Make sure it is there on all submit and exec hosts and give it world read and write permissions.

Anup

On Sep 17, 2010, at 8:34 AM, "Julian Krauskopf" <[hidden email]> wrote:

> The jobs are running local without an installed DCE
> I allready pasted this command into the shell and it works. so the command must be correct.
>
> Now i get this error on pipeline.xml.run.out:
>
>
> 17:56:04:612 [Thread: ID:10647 - train for glimmer3 iteration] SGEMockServer submit:363  Couldn't create directory needed by server /working/0
> WARN 17:56:04:613 [Thread: ID:10647 - train for glimmer3 iteration] CommandProcessor executeCommand:201 Caught Exception for
> FATAL 17:56:04:639 [Thread: ID:10647 - train for glimmer3 iteration] ExceptionHandler handleExceptionQuietMode:137 Config error, /working/0could not be created
>
> java.io.IOException: Config error, /working/0could not be created
>    at org.tigr.htc.request.SGEMockServer.submit(SGEMockServer.java:366)
>    at org.tigr.htc.request.HTCRequest.submit(HTCRequest.java:209)
>    at org.tigr.workflow.common.DistributedProcessor.submitHTCRequest(DistributedProcessor.java:258)
>    at org.tigr.workflow.common.DistributedProcessor.process(DistributedProcessor.java:147)
>    at org.tigr.workflow.common.CommandProcessor.executeCommand(CommandProcessor.java:167)
>    at org.tigr.workflow.common.CommandProcessor.run(CommandProcessor.java:271)
>    at org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:243)
>    at org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:222)
>    at org.tigr.antware.shared.concurrent.ThreadPoolWorker.access$000(ThreadPoolWorker.java:26)
>    at org.tigr.antware.shared.concurrent.ThreadPoolWorker$1.run(ThreadPoolWorker.java:102)
>    at java.lang.Thread.run(Thread.java:619)
> Config error, /working/0could not be created
>
>
> Julian
> --
> Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!  
> Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Julian Krauskopf
In reply to this post by Julian Krauskopf
i just reinstalled ergatis to make sure that there are no complication with the isga patch. But now i get another error within the train_for_glimmer3 component.

the command is

 /opt/ergatis/bin/train_for_glimmer3_iteration --input_predict_list=/usr/local/projects/test/output_repository/glimmer3/4_iter1/glimmer3.raw.list --input_fasta_list=/usr/local/projects/test/output_repository/split_multifasta/4_default/split_multifasta.fsa.list --output_pwm=/usr/local/projects/test/output_repository/train_for_glimmer3_iteration/4_train_for_glimmer/all.motif --tmp_dir=/usr/local/scratch/new/train_for_glimmer3_iteration/4_train_for_glimmer --glimmer3_dir=/opt/glimmer3 --elph_bin=/opt/ELPH/sources/elph --conf_ini_file=/usr/local/projects/test/workflow/runtime/glimmer3/4_iter2/glimmer3.iter2.user.config

and the error

return value: 127
message: Error executing script exit value: 127awk: /opt/glimmer3/scripts/upstream-coords.awk:26: fatal: cannot open file `/usr/local/scratch/new/train_for_glimmer3_iteration/4_train_for_glimmer/gi' for reading (No such file or directory) sh: 169235049: command not found sh: ref: command not found sh: NC_010364.1: command not found sh: .coords: command not found ERROR: Could not open file /usr/local/scratch/new/train_for_glimmer3_iteration/4_train_for_glimmer/gi errno = 2 sh: 169235049: command not found sh: ref: command not found sh: NC_010364.1: command not found sh: .coords: command not found Died with '/opt/glimmer3/bin/start-codon-distrib -3 /usr/local/projects/test/output_repository/split_multifasta/4_default/i1/g1/gi_169235049_ref_NC_010364.1_.fsa /usr/local/scratch/new/train_for_glimmer3_iteration/4_train_for_glimmer/gi|169235049|ref|NC_010364.1|.coords returned nothing' at /opt/ergatis/bin/train_for_glimmer3_iteration.pl line 129

when i run this command through the shell i get the same error. must be some problem with the file '/gi|169235049|ref|NC_010364.1|.coords'

thanks for any help
Julian
--
GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 Euro/mtl.!*
http://portal.gmx.net/de/go/dsl

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users
Reply | Threaded
Open this post in threaded view
|

Re: train_for_glimmer3_iteration

Chris Hemmerich
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users