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 > --*-- -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: [email protected] Web: http://www.pharmaceutical-bioinformatics.org/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
