Hi, I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I've run into the following error: ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist. I see via much googling that this error is due to a user input problem. I've tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files: hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa where the following files exist: hg19.dict hg19.fa hg19.fa.fai I'm using a torque setup. A bam file is being used as input. After much trial and error I've been unable to figure out what I'm missing. None of the solutions on google apply to my situation. Has anyone else run into this configuration problem and solved it? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand@ssc-spc.gc.ca
Hi, do you have access to the generated commandline from Galaxy and can paste it her?
I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I’ve run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder? Cheers, Bjoern
I’m using a torque setup. A bam file is being used as input. After much trial and error I’ve been unable to figure out what I’m missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Bjoern, The loc file is tabular. I put the 2bit file in the directory and had no success. Here is the rather lengthy commandline: #!/bin/sh export GALAXY_SLOTS_CONFIGURED="1" if [ -n "$SLURM_JOB_NUM_NODES" ]; then GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED fi export GALAXY_SLOTS GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh; PACKAGE _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_ settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout "/software/packages/galaxy/galaxy-dist/da tabase/files/000/dataset_126.dat" -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114. dat" "bam" "gatk_input" -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta data_19.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "Rea lignerTargetCreator" -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat" $GATK2_S ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads ${GALAXY_SLOTS:-4} -R "" '; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/ galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code" echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec Thanks, -Sheldon -----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 12:26 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2 Hi, do you have access to the generated commandline from Galaxy and can paste it her?
I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I’ve run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder? Cheers, Bjoern
I’m using a torque setup. A bam file is being used as input. After much trial and error I’ve been unable to figure out what I’m missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED="1" if [ -n "$SLURM_JOB_NUM_NODES" ]; then GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED fi
export GALAXY_SLOTS GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi
[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh; PACKAGE _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_ settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout "/software/packages/galaxy/galaxy-dist/da tabase/files/000/dataset_126.dat" -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114. dat" "bam" "gatk_input" -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta data_19.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "Rea lignerTargetCreator" -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat" $GATK2_S ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads ${GALAXY_SLOTS:-4}
-R ""
-> that is the error. Here needs to be your path to the fasta file. Can you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome" Can you attach your gatk2_picard_index.loc? Thanks, Bjoern
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/ galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code" echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
Thanks, -Sheldon
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 12:26 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2
Hi,
do you have access to the generated commandline from Galaxy and can paste it her?
I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I’ve run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder?
Cheers, Bjoern
I’m using a torque setup. A bam file is being used as input. After much trial and error I’ve been unable to figure out what I’m missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
We do see hg19 in the reference genome box. We are using revision 8bcc13094767 of the GATK2 wrapper. The only line in the .loc file is the one listed in my first email. I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated. Thanks! -Sheldon -----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 1:33 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2 Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED="1" if [ -n "$SLURM_JOB_NUM_NODES" ]; then GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED fi
export GALAXY_SLOTS GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi
[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc /gatk2/8bcc13094767/env.sh; PACKAGE _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_setting s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_ settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout "/software/packages/galaxy/galaxy-dist/da tabase/files/000/dataset_126.dat" -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114. dat" "bam" "gatk_input" -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta data_19.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "Rea lignerTargetCreator" -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat" $GATK2_S ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads ${GALAXY_SLOTS:-4}
-R ""
-> that is the error. Here needs to be your path to the fasta file. Can you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome" Can you attach your gatk2_picard_index.loc? Thanks, Bjoern
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/ galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1 02_DXIvP5,/software/packages/galaxy/galaxy-dis t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA ssociation_102_ifJAbu,/software/packages/galax y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist oryDatasetAssociation_102_Ie2O0C,/software/pac kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada ta_results_HistoryDatasetAssociation_102_xLNtK a,,/software/packages/galaxy/galaxy-dist/database/job_working_director y/000/101/metadata_override_HistoryDatasetAsso ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101/metadata_in_HistoryD atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat abase/job_working_directory/000/101/metadata_k wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal axy-dist/database/job_working_directory/000/10 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages /galaxy/galaxy-dist/database/job_working_direc tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s oftware/packages/galaxy/galaxy-dist/database/j ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code" echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
Thanks, -Sheldon
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 12:26 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2
Hi,
do you have access to the generated commandline from Galaxy and can paste it her?
I’ve installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I’ve run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I’ve tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder?
Cheers, Bjoern
I’m using a torque setup. A bam file is being used as input. After much trial and error I’ve been unable to figure out what I’m missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I have no clue what is happening. Attached is my working *.loc flile. See select-box is also filtered by the db-key of your dataset, but I think you habe hg19 as dbkey, otherwise you would not see the hg19 in the select box. There must be something wrong in you *.log file. 2014-01-30 Briand, Sheldon <Sheldon.Briand@ssc-spc.gc.ca>:
We do see hg19 in the reference genome box. We are using revision 8bcc13094767 of the GATK2 wrapper. The only line in the .loc file is the one listed in my first email. I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated.
Thanks! -Sheldon
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 1:33 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2
Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED="1" if [ -n "$SLURM_JOB_NUM_NODES" ]; then GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED fi
export GALAXY_SLOTS GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi
[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc /gatk2/8bcc13094767/env.sh; PACKAGE _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_setting s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_ settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout "/software/packages/galaxy/galaxy-dist/da tabase/files/000/dataset_126.dat" -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114. dat" "bam" "gatk_input" -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta data_19.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "Rea lignerTargetCreator" -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat" $GATK2_S ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads ${GALAXY_SLOTS:-4}
-R ""
-> that is the error. Here needs to be your path to the fasta file. Can you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome"
Can you attach your gatk2_picard_index.loc?
Thanks, Bjoern
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/ galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1 02_DXIvP5,/software/packages/galaxy/galaxy-dis t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA ssociation_102_ifJAbu,/software/packages/galax y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist oryDatasetAssociation_102_Ie2O0C,/software/pac kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada ta_results_HistoryDatasetAssociation_102_xLNtK a,,/software/packages/galaxy/galaxy-dist/database/job_working_director y/000/101/metadata_override_HistoryDatasetAsso ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101/metadata_in_HistoryD atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat abase/job_working_directory/000/101/metadata_k wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal axy-dist/database/job_working_directory/000/10 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages /galaxy/galaxy-dist/database/job_working_direc tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s oftware/packages/galaxy/galaxy-dist/database/j
echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
Thanks, -Sheldon
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 12:26 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2
Hi,
do you have access to the generated commandline from Galaxy and can
ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code" paste it her?
I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I've run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I've tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder?
Cheers, Bjoern
I'm using a torque setup. A bam file is being used as input. After much trial and error I've been unable to figure out what I'm missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca
___________________________________________________________ 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: http://lists.bx.psu.edu/
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Hi, Thanks for your help. It turns out an extra carriage return snuck into the end of the .loc file. Once I removed that everything worked. -Sheldon From: bjoern.gruening@googlemail.com [mailto:bjoern.gruening@gmail.com] Sent: Thursday, January 30, 2014 2:05 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] GATK2 I have no clue what is happening. Attached is my working *.loc flile. See select-box is also filtered by the db-key of your dataset, but I think you habe hg19 as dbkey, otherwise you would not see the hg19 in the select box. There must be something wrong in you *.log file. 2014-01-30 Briand, Sheldon <Sheldon.Briand@ssc-spc.gc.ca<mailto:Sheldon.Briand@ssc-spc.gc.ca>>: We do see hg19 in the reference genome box. We are using revision 8bcc13094767 of the GATK2 wrapper. The only line in the .loc file is the one listed in my first email. I've put that line in both tool-data and tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767<http://toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767> loc files. We didn't see the reference genome hg19 until the loc file for the repo was populated. Thanks! -Sheldon -----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Thursday, January 30, 2014 1:33 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] GATK2 Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED="1" if [ -n "$SLURM_JOB_NUM_NODES" ]; then GALAXY_SLOTS="$SLURM_JOB_NUM_NODES" elif [ -n "$NSLOTS" ]; then GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED fi
export GALAXY_SLOTS GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH" else PYTHONPATH="$GALAXY_LIB" fi export PYTHONPATH fi
[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc /gatk2/8bcc13094767/env.sh; PACKAGE _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_setting s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh; PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; . /software/packages/galaxy/galaxy-dist/dependancies/environment_ settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python /software/packages/galaxy/shed_tools/toolshed.g2.b x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py<http://x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py> --stdout "/software/packages/galaxy/galaxy-dist/da tabase/files/000/dataset_126.dat" -d "-I" "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114. dat" "bam" "gatk_input" -d "" "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta data_19.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "Rea lignerTargetCreator" -o "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat" $GATK2_S ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads ${GALAXY_SLOTS:-4}
-R ""
-> that is the error. Here needs to be your path to the fasta file. Can you point to me to Tool Shed Version you are using and are you running the latest revision? Do you see hg19 / hg18 in the select-box under "using-reference genome" Can you attach your gatk2_picard_index.loc? Thanks, Bjoern
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist; /software/packages/galaxy/galaxy-dist/set_metadata.sh ./database/files /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/ galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json /software/packages/galaxy/galaxy-dist/database /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1 02_DXIvP5,/software/packages/galaxy/galaxy-dis t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA ssociation_102_ifJAbu,/software/packages/galax y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist oryDatasetAssociation_102_Ie2O0C,/software/pac kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada ta_results_HistoryDatasetAssociation_102_xLNtK a,,/software/packages/galaxy/galaxy-dist/database/job_working_director y/000/101/metadata_override_HistoryDatasetAsso ciation_102__IZJ7Y /software/packages/galaxy/galaxy-dist/database/job_working_directory/0 00/101/metadata_in_HistoryD atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat abase/job_working_directory/000/101/metadata_k wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal axy-dist/database/job_working_directory/000/10 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages /galaxy/galaxy-dist/database/job_working_direc tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s oftware/packages/galaxy/galaxy-dist/database/j ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY; sh -c "exit $return_code" echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec<http://101.ec>
Thanks, -Sheldon
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>] Sent: Thursday, January 30, 2014 12:26 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] GATK2
Hi,
do you have access to the generated commandline from Galaxy and can paste it her?
I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I've run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist.
I see via much googling that this error is due to a user input problem. I've tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files:
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
That look ok, as far as every token is separated by a tabular.
where the following files exist:
hg19.dict
hg19.fa
hg19.fa.fai
Can you put the 2bit file into the same folder?
Cheers, Bjoern
I'm using a torque setup. A bam file is being used as input. After much trial and error I've been unable to figure out what I'm missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
Thanks,
-Sheldon
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
902 426-1677
sheldon.briand@ssc-spc.gc.ca<mailto:sheldon.briand@ssc-spc.gc.ca>
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
bjoern.gruening＠googlemail.com -
Björn Grüning
-
Briand, Sheldon