Hi Kelly, On 06/24/2011 08:40 PM, Kelly Vincent wrote:

That particular tool uses a different loc file--all_fasta.loc, which is simply a list of fasta files with full path/name. Are your other Picard tools working? Let us know if you run into further issues.

thank you. Now the indices show up, moreover the picard tools seem to work (didn't test the modules related to PAIRED data yet). One thing that doesn't work is the sorting in the "SAM/BAM Alignment Summary Metrics" module. When I turn off "Assume the input file is already sorted", galaxy tries to sort the bam file first. Job state ends in green in the history, but the Picard Tool Run Log contains 'Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /local/data/galaxy_files/000/dataset_248.dat.sorted at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:51)' (full log at the bottom). Looking in the respective directory there is the file "dataset_248.dat.sorted.bam" though. It looks like the picard wrapper expects that the .bam-suffix is not on the file. Regards, Holger --->%--- "INFO:root:## executing samtools sort /local/data/galaxy_files/000/dataset_248.dat /local/data/galaxy_files/000/dataset_248.dat.sorted returned status 0 and nothing on stderr INFO:root:## executing java -Xmx4g -jar /local/data/home/galaxy/galaxy-dist/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=false ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/local/data/home/galaxy/galaxy-dist/database/job_working_directory/220/dataset_254_files/CollectAlignmentSummaryMetrics.metrics.txt R=/local/data/home/galaxy/galaxy-dist/database/job_working_directory/220/dataset_254_files/hg19full.fa_fake.fasta TMP_DIR=/tmp INPUT=/local/data/galaxy_files/000/dataset_248.dat.sorted returned status 1 and stderr: [Mon Jun 27 12:04:54 CEST 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/local/data/galaxy_files/000/dataset_248.dat.sorted OUTPUT=/local/data/home/galaxy/galaxy-dist/database/job_working_directory/220/dataset_254_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/local/data/home/galaxy/galaxy-dist/database/job_working_directory/220/dataset_254_files/hg19full.fa_fake.fasta ASSUME_SORTED=false TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Jun 27 12:04:54 CEST 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2058027008 Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /local/data/galaxy_files/000/dataset_248.dat.sorted at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:51) at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:65) at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118) at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) ---%<---

Thanks, Kelly

On Fri Jun 24, at 7:44 AM, Holger Klein wrote:

...

Dear all,

I have a problem setting up the reference genomes for picard. They simply do not show up. I used revision 8c11dd28a3cf of galaxy-dist and just today switched to 720455407d1c, problem still exists.

My picard_index.loc contains the following lines: hg19full hg19 hg19 Full /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa hg18full hg18 hg18 Full /home/galaxy/galaxy-data/index_files/hg18/picard_index/hg18.fa mm9full mm9 mm9 Full /home/galaxy/galaxy-data/index_files/mm9/picard_index/mm9.fa

The respective files are also there (fa and fa.fai are links to the respective files in other dirs): /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.dict /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa /home/galaxy/galaxy-data/index_files/hg19/picard_index/hg19full.fa.fai

Now, using e.g. the SAM/BAM Alignment Summary Metrics module from Picard, I can't choose a reference genome (no matter if it's "use assigned ref genome" or "select a different built-in genome").

It doesn't seem to be a problem of formatting or file permissions - the srma module needs the picard generated indices as well, the entries are exactly the same and there it works.

Does anyone have a hint on how to get this working?

Regards, Holger

-- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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-- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511