Hi Sarah,

I'll try to debug, point per point:

>>> - Here is the error I get when running the tool FilterControl 
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007fe56800ecd0 ***

I think here you have a misconfiguration of the memory of your java install 
(according to the need of the tool)

If you look at the FilterControlPeaks.sh file, the java is called with the 
option -Xmx6g. So your java install have to be allowed to use 6G as memory (by 
default it's 1024M)

>>> - Here is the error I get when running the tool IntersectBed 
>>> 
>>> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe
>>> près du symbole inattendu « ;; »
>>> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect
>>> -f 0.05

I don't understand this one, The intersectBed tool is only composed of a xml 
which simply call bedtools..

Check the command by typing 'bedtools intersect' in a terminal, if it sends you 
back the option list, the Galaxy tool should work.. If not, you have to check 
your bedtools install

>>> - Here is the error I get when running the tool ChIPmunk (thanks Alban
>>> for you help (ChIPMunk v2 is used and all librairies are found) but
>>> here is a new error, maybe a problem of "dirname" ?)
>>> 
>>> mv: impossible d'évaluer
>>> « 
>>> /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png
>>>  »: Aucun fichier ou dossier de ce type
>>> mv: impossible d'évaluer « /work/gala
Here, I think that the error is due to the ChIPMunk execution which doesn't 
work.

You can try the ChIPMunk execution this way:

Find the line containing:

ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 s:$inputfile 
100 10 1 4 >> /dev/null 2>> /dev/null

Add a line with:

echo "ruby $CHIPMUNK_BIN_DIR/run_chiphorde.rb $LOG $motifs $MODE yes 1.0 
s:$inputfile 100 10 1 4 >> /dev/null 2>> /dev/null" > ~/ChIPMunk.log

Then try to launch the command in ~/ChIPMunk.log in a terminal and look at the 
output.

If ChIPMunk has run, the error comes from next step (i.e. the 
parseChipmunkOutput.pl script).

Else, try to debug ChIPMunk, and then the tool will work.
>>> 
>>> 
>>> - Here is the error I get when running the tool PeaksToBed 
>>> readline() on closed filehandle FILE at
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 124 (#1)
>>>     (W closed) The filehandle you're reading from got itself closed sometime
>>>     before now.  Check your control flow.
>>>     
>>> Use of uninitialized value $fields[1] in concatenation (.) or string at

For this one, edit the PeaksToBed.pl script this way:

The 3 lines:

use strict;
use warnings;
use diagnostics;

becomes:

#use strict;
#use warnings;
#use diagnostics;

Galaxy doesn't really love to have the return of a script (even if it's not an 
error). Here the perl scripts gives you warnings that are understood as errors 
by Galaxy.


Hope It will help you, don't hesitate if you need more..

++,

Alban



--
Alban Lermine
Unité 900: INSERM - Mines ParisTech - Institut Curie
" Bioinformatics and Computational Systems Biology of Cancer"
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel: +33 (0) 1 56 24 69 84



Le 1 févr. 2013 à 14:41, Sarah Maman <sarah.ma...@toulouse.inra.fr> a écrit :

> Thanks Bjoern,
> 
> In your xml file, I 've specified the interpreter :
> <command> replace by <command interpreter="bash"> but the problem is not 
> solved (";" is supported by our cluster) because the command is runned with 
> an error ";;" (double ;) instead of ";" (simple ;) :
> `bash /my/path/to/RepeatMasker -parallel 8         -species fungi   -dir 
> /work/tmp/tmprRrJh2      -gff   
> /my/path/to/galaxy/database/files/005/dataset_5979.dat   > /dev/null 2> 
> /dev/null;      
> cp /my/path/to/work/tmp/tmprRrJh2/dataset_5979.dat.tbl 
> /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5999.dat;
>       
> cp /work/tmp/tmprRrJh2/dataset_5979.dat.out.gff None;   
> cp /work/tmp/tmprRrJh2/dataset_5979.dat.masked None; 
> tail -n +4 /work/tmp/tmprRrJh2/dataset_5979.dat.out | tr -s ' ' '\t' > 
> /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5998.dat;
>   
> rm /work/tmp/tmprRrJh2 -r;; 
> cd /my/path/to/galaxy/galaxy-dist;
> /my/path/to/galaxy/galaxy-dist/set_metadata.sh 
> /my/path/to/galaxy/database/files 
> /my/path/to/galaxy/database/job_working_directory/004/4135 . 
> /my/path/to/galaxy/galaxy-dist/universe_wsgi.ini 
> /work/tmp/tmpi0u8TZ 
> /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy.json 
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_in_HistoryDatasetAssociation_6156_Lp_2X3,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_kwds_HistoryDatasetAssociation_6156_emJ62i,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_out_HistoryDatasetAssociation_6156_Dgw3la,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_results_HistoryDatasetAssociation_6156_aTCjOU,
> /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5999.dat,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_override_HistoryDatasetAssociation_6156_I6enyB
>  
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_in_HistoryDatasetAssociation_6155_LRm2gT,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_kwds_HistoryDatasetAssociation_6155_4xAztH,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_out_HistoryDatasetAssociation_6155_14AYvT,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_results_HistoryDatasetAssociation_6155_l_1gJ2,
> /my/path/to/galaxy/database/job_working_directory/004/4135/galaxy_dataset_5998.dat,
> /my/path/to/galaxy/database/job_working_directory/004/4135/metadata_override_HistoryDatasetAssociation_6155_NufEns'
> So the error is ";;"
> rm /work/tmp/tmprRrJh2 -r;; 
> instead of ";"
> rm /work/tmp/tmprRrJh2 -r;
> I've tried to replace ";" by nothing but this generate others errors (files 
> not generated) :
> cp: impossible d'évaluer « /work/tmp/tmpga_QOo/dataset_5979.dat.tbl »: Aucun 
> fichier ou dossier de ce type
> cp: impossible d'évaluer « /work/tmp/tmpga_QOo/dataset_5979.dat.out.gff »: 
> Aucun fichier ou dossier de ce type
> cp: impossible d'évaluer « /work/tmp/tmpga_QOo/dataset_5979.dat.masked »: 
> Aucun fichier ou dossier de ce type
> tail: impossible d'ouvrir « /work/tmp/tmpga_QOo/dataset_5979.dat.out » en 
> lecture: Aucun fichier ou dossier de ce type
> Do you have any idea ?
> Thanks in advance,
> Sarah
> 
> 
> 
> 
> Björn Grüning a écrit :
>> 
>> Hi Sarah,
>> 
>> i looks like something is wrong with the PBS system.
>> The errors for bedtools and repeatmasker are the same. I can't
>> understand french but i guess that ";" are not supported by PBS or in
>> your configuration? Repeatmasker and bedtools creating more than one
>> shell command and concatenating them with ';'.
>> 
>> Hope that helps,
>> Bjoern
>> 
>>   
>>> Hello,
>>> 
>>> I've installed NEBULA tools and "RepeatMasker" tool on our local
>>> Galaxy instance.
>>> 
>>> For some tools (others work), I get the following errors:
>>> - Here is the error I get when running the tool FilterControl 
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007fe56800ecd0 ***
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007fe56800ecd0 ***
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007fe56800ecd0 ***
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007fe56800ecd0 ***
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh:
>>>  line 80: 61310 Abandon                 java -classpath $LOCAL_PATH/ -Xmx6g 
>>> FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o 
>>> $output > /dev/null
>>> *** glibc detected *** java: double free or corruption (!prev): 
>>> 0x00007f1f5800ecd0 ***
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh:
>>>  line 81: 61351 Abandon      
>>> 
>>> - Here is the error I get when running the tool IntersectBed 
>>> 
>>> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe
>>> près du symbole inattendu « ;; »
>>> /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect
>>> -f 0.05
>>> 
>>> - Here is the error I get when running the tool ChIPmunk (thanks Alban
>>> for you help (ChIPMunk v2 is used and all librairies are found) but
>>> here is a new error, maybe a problem of "dirname" ?)
>>> 
>>> mv: impossible d'évaluer
>>> « 
>>> /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png
>>>  »: Aucun fichier ou dossier de ce type
>>> mv: impossible d'évaluer « /work/gala
>>> 
>>> 
>>> - Here is the error I get when running the tool PeaksToBed 
>>> readline() on closed filehandle FILE at
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 124 (#1)
>>>     (W closed) The filehandle you're reading from got itself closed sometime
>>>     before now.  Check your control flow.
>>>     
>>> Use of uninitialized value $fields[1] in concatenation (.) or string at
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 154, <FILE> line 1 (#2)
>>>     (W uninitialized) An undefined value was used as if it were already
>>>     defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.
>>>     To suppress this warning assign a defined value to your variables.
>>>     
>>>     To help you figure out what was undefined, perl will try to tell you the
>>>     name of the variable (if any) that was undefined. In some cases it 
>>> cannot
>>>     do this, so it also tells you what operation you used the undefined 
>>> value
>>>     in.  Note, however, that perl optimizes your program and the operation
>>>     displayed in the warning may not necessarily appear literally in your
>>>     program.  For example, "that $foo" is usually optimized into "that "
>>>     . $foo, and the warning will refer to the concatenation (.) operator,
>>>     even though there is no . in your program.
>>>     
>>> Use of uninitialized value in concatenation (.) or string at
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 154, <FILE> line 1 (#2)
>>> Use of uninitialized value in numeric ge (>=) at
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 156, <FILE> line 1 (#2)
>>> ......
>>>     
>>> /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl 
>>> line 156, <FILE> line 63 (#2)
>>> 
>>> Use of uninitialized value $fields[1] in conc
>>> 
>>> 
>>> I dowloaded tool "RepeatMasker" from Galaxy Tool Shed,and RepeatMasker
>>> is installed on our cluster.
>>> Here is the error I get when running the tool RepeatMasker:
>>> 
>>> An error occurred running this job: Epilog : job finished at jeu.
>>> janv. 31 14:39:16 CET 2013
>>> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe
>>> près du symbole inattendu « ;; »
>>> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker
>>> -parallel 8 -speci
>>> 
>>> 
>>> Do you have any ideas ?
>>> Thank you in advance for your help,
>>> Sarah Maman 
>>> -- 
>>>           --*--
>>> Sarah Maman
>>> INRA - LGC - SIGENAE
>>> http://www.sigenae.org/
>>> Chemin de Borde-Rouge - Auzeville - BP 52627
>>> 31326 Castanet-Tolosan cedex - FRANCE
>>> Tel:   +33(0)5.61.28.57.08
>>> Fax:   +33(0)5.61.28.57.53 
>>>          --*--
>>>     
>> 
>>   
> 
> 
> -- 
>           --*--
> Sarah Maman
> INRA - LGC - SIGENAE
> http://www.sigenae.org/
> Chemin de Borde-Rouge - Auzeville - BP 52627
> 31326 Castanet-Tolosan cedex - FRANCE
> Tel:   +33(0)5.61.28.57.08
> Fax:   +33(0)5.61.28.57.53 
>          --*--

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