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
--*--