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snpEf dataset generation errors
by Iry Witham 09 Oct '14

09 Oct '14

I am trying to resolve an issue with snpEff 3.4 running on a cloudman instance of galaxy. The instance is invoking the following command and failing: java -Xmx6G -jar $SNPEFF_JAR_PATH/snpEff.jar eff -c $SNPEFF_JAR_PATH/snpEff.config -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /mnt/galaxy/files/000/dataset_364.dat -noLog -download GRCh37.68 /mnt/galaxy/files/000/dataset_313.dat > /mnt/galaxy/files/000/dataset_363.dat The error it is reporting is: Fatal error: Exit code 255 (Error) java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:159) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:234) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:217) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:122) ... 8 more java.lang.RuntimeException: Genome download failed! at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1002) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I have upgraded to java 1.7.0 due to an issue with GATK2. In addition to this when I try to run snpEff I am unable to select a genome source unless I use the "Named on demand" option. How do I get snpEff genome version data configured? The snpEff_genomes.loc file lists all of the genomes I need and many more. I appreciate the help. Regards, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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CloudMan: Autoscaling =Unable to run this job due to a cluster error
by Petit III, Robert A. 09 Oct '14

09 Oct '14

Hello Galaxy Team! I've set up a vanilla CloudMan instance using AWS. I've set the head node to not handle jobs and have set AutoScaling to a minimum of 0 and a maximum of 4 worker nodes. Upon submitting a job, it fails with the following error: Unable to run this job due to a cluster error, please retry it later Now if I set AutoScaling to a minimum of 1 worker node it works fine. But I would rather not always have 1 worker node up. Any recommendations? Thank you very much, Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Download tool-dependency with using a proxy and functional tests http 403 error
by Marcus.Jaeger＠kws.com 09 Oct '14

09 Oct '14

Hi, I have two problems and I hope you can help me. The first one is, I can't download a package within the tool-dependency description, because our company uses a proxy. How can I define using a proxy in the "tool_dependencies.xml" file? The second one is, I try to run functional tests in our toolshed. But I got a http 403 error. I followed these steps to run the tests: https://wiki.galaxyproject.org/InstallAndTestCertification (in chapter: Using the Install and Test Framework With a Local Tool Shed) When I run the test, it got stuck when installing the testing tool to the temporary galaxy instance. But it is possible to access the temporary galaxy instance in a webbrowser. I found out, that the temporary database is empty and doesn't include any user. So i think that could be the reason for the http 403 error? Can you please give me advice how to resolve these issues? Thank you very much. - marcus

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GATK2 reporting "Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8."
by Iry Witham 09 Oct '14

09 Oct '14

Hi Team, I have installed GATK2 into a galaxy cloud instance to use the Unified Genotyper for our sequencing course. However, when I run the tool I get the following error message: Dataset 41: Unified Genotyper on data 8 and data 13 (VCF) Tool execution generated the following error message: ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.2-2-gec30cee): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions http://www.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8. ERROR ------------------------------------------------------------------------------------------ The following is the command that is being invoked by galaxy: python /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/gatk2_wrapper.py --stdout "/mnt/galaxy/files/000/dataset_326.dat" -d "-I" "/mnt/galaxy/files/000/dataset_226.dat" "bam" "gatk_input_0" -d "" "/mnt/galaxy/files/_metadata_files/000/metadata_13.dat" "bam_index" "gatk_input_0" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads ${GALAXY_SLOTS:-4} --out "/mnt/galaxy/files/000/dataset_324.dat" --metrics_file "/mnt/galaxy/files/000/dataset_325.dat" $GATK2_SITE_OPTIONS --num_cpu_threads_per_data_thread 1 --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" ' -d "-R" "/mnt/galaxy/files/000/dataset_220.dat" "fasta" "gatk_input" I have reviewed my configuration files and cannot locate where the issue lies. I am also posting this with the GATK Forum to see if they have any ideas. Unfortunately I need to get this resolved ASAP since I need to complete my testing by tomorrow. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
by Chris Dagdigian 09 Oct '14

09 Oct '14

Hi folks, Got a strange problem - it's hit me on all my self-install options today including using the Chef cookbook as well as the galaxy mecurial install method on Ubuntu 12.04 LTS I'm trying to build a local galaxy that supports a few common extra tools (things like samtools etc.) I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at getgalaxy.org: > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > cd galaxy-dist > hg update stable sh ./run.sh There are two strange things that don't quite match what I'm expecting to see from the docs ... (1) The file "universe_wsgi.ini " no longer gets created in galaxy-dist/ after running "run.sh" for the first time. This is strange because I remember it working days ago but now on fresh server and fresh checkout the file does not get created and I have to manually create one in oder to set "host = 0.0.0.0" (2) I can't even install simple tools like samtools from the standard tool sheds. The status page gets stuck at "installing dependencies" and if I navigate away I get a browser javascript error ("Initializing repository installation failed" Any tips or tricks appreciated, thanks! Regards, Chris

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ToolShed tool preview broken (TestToolShed too)
by Peter Cock 08 Oct '14

08 Oct '14

Hi all, >From the "new tools" information Dave Compiled for the last Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions I had a look at galaxyp's "filter_by_fasta_ids: Extract sequences from a FASTA file based on a list of IDs" tool: https://toolshed.g2.bx.psu.edu/view/galaxyp/filter_by_fasta_ids I wanted to see how it compared to my own similar tools (which handle FASTA, FASTQ, SFF and could cover more - they replaced my older single format filter tools): https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id Now for the bug report, clicking on the button (under valid tools) which would normally give a preview of the tool form is failing - giving just "Internal Server Error". I have tried a random selection of other tools and this seems to be universal - moreover the TestToolShed also seems to have the same problem. Regards, Peter

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testtoolshed internal server error
by Stef van Lieshout 08 Oct '14

08 Oct '14

Anyone else getting this when trying to upload to a testtoolshed repos? I'm using the "upload files to repository" function in "repository actions" and get a blank page with "internal server error".. Worked fine yesterday. Ciao, Stef

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Internal Server Error on metadata reset
by Saket Choudhary 07 Oct '14

07 Oct '14

I am trying to reset metadata on all my repositories at once using the "Reset metadata on my repositories" button on https://testtoolshed.g2.bx.psu.edu/ It fails with: Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/reset_metadata_on_my_writable_… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2795 inreset_metadata_on_my_writable_repositories_in_tool_shed >> my_writable=True ) Module tool_shed.metadata.repository_metadata_manager:65 in build_repository_ids_select_field >> query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable,order=True ) Module tool_shed.metadata.repository_metadata_manager:513 in get_query_for_setting_metadata_on_repositories >> .filter( or_( *clause_list ) ) NameError: global name 'or_' is not defined extra data

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Cloudman indices installation/configuration
by Iry Witham 07 Oct '14

07 Oct '14

Hi Team, I have a new instance of galaxy cloudman running and have added tools from the toolshed to it. When I attempt to run tools like sam-to-bam or any gatk tool I am prompted for a reference genome. However, indices/references not available for these tools. I have added the following line to the sam_fa_indices.loc, but that did nothing: index hg19 /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa I have also added the following three lines to the gatk2_picard_index.loc: hg19 hg19 Human (hg19) /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa GRCh37 GRCh37 Human (GRCh37) /mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa mm10 mm10 Mouse (mm10) /mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa I know I have missed something, but can't seem to figure it out. Could someone point me in the right direction? Regards, __________________________________ Iry T. Witham Scientific Applications Administrator Computational Sciences Group The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org [cid:A4FA2ADE-F7C3-4B38-851C-6FE20C32198B] The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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clustalomega from toolshed installation issue
by Isabelle Phan 07 Oct '14

07 Oct '14

Hello, I installed clustalomega from the galaxy main toolshed using the admin interface of our local galaxy install. When I run the tool, I get this message: Dataset generation errors Dataset 55: co_alignment.fasta Tool execution generated the following error message: Error invoking command: clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o /opt/galaxy-dist/database/files/000/dataset_158.dat -l /opt/galaxy-dist/database/files/000/dataset_159.dat -v -i /opt/galaxy-dist/database/files/000/dataset_153.dat [Errno 2] No such file or directory I've tried reloading my input file, reloading the tool's configuration, resetting the metadata on the clustalomega repository, deleting the tool completely and re-installing. No luck. If I try to rerun the job again, I get non-sensical errors that seem to originate from other tools, as if the database was completely garbled. Each of those tools work fine. Only clustalomega behaves oddly. I have no access to our galaxy server, so any solution would have to be implemented from the admin interface. thanks for any hints, Isabelle

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