FW: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk
Hi Jen, thanks. I am a bit confused: on Galaxy the only human genome listed is hg_g1k_v37. So when I uploaded the new data from "Get data", under "Genome" I selected hg_g1k_v37 Now, all i want is to get cufflinks with gene names: which genome am I supposed to use? the only one I knew was hg19 from iGenomes...but seems i cannot use it. Do I have to select a genome when I upload raw fastq data? I havent stated doign anything so far, its just raw data Thanks a lot, Irene ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Wednesday, November 27, 2013 10:08 PM To: Irene Bassano Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk Hello, iGenomes covers the UCSC build, and this named "Human Feb. 2009 (GRCh37/hg19) (hg19)" in the full name in the UI. The "hg19" key is the important part - as the name may be abbreviated in some tools, but this key will be in all. The genome with the "hg_g1k_v37" key is slightly different and you will have another genome mismatch problem with the RNA-seq (and most other) tools if you combine this genome with data from UCSC (the source of hg19) or the wrong iGenomes file. "hg_g1k_v37" (source: 1000 genomes via GATK) and "hg19" (source: UCSC) are just about the same, but the identifiers are different. If you want to examine the differences, both are available on our rsync server and can be downloaded and compared. On the "Help -> Support" wiki are links for reference genomes. The iGenomes GTF file for hg19 is on the public Main server, if that is more convenient for you, or should you just want to be sure you have the right one. Look in Shared Data -> Data Libraries -> iGenomes. Best, Jen Galaxy team ps. please try to send new questions to one of our lists, thanks! On 11/27/13 12:51 PM, Irene Bassano wrote:
Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list ""Homo sapiens b37(hg_g1k_v37).
Is this the same as the genome listed in UCSC "February 2009 (GRCh37/hg19)"?
I am using iGenomes to get the gene names rather than annotation such as NM_00xxxx and I fused the UCSC website choosing the newest genome, February 2009
Thanks,
best, Irene ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Monday, November 18, 2013 7:26 PM To: galaxy-bugs@bx.psu.edu; Irene Bassano Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk
Hi again,
The database mismatch is a problem here is well for the same reasons. My guess is that you intended to run dataset #21 against hg19, and that the run against hg18 was a tool form input mistake?
Good luck with the next runs,
Jen Galaxy team
On 11/18/13 5:21 AM, galaxy-bugs@bx.psu.edu wrote:
GALAXY TOOL ERROR REPORT ------------------------
This error report was sent from the Galaxy instance hosted on the server "usegalaxy.org" ----------------------------------------------------------------------------- This is in reference to dataset id 7081835 from history id 1686699 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item
37: Cufflinks on data 21 and data 34: assembled transcripts
by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.
usegalaxy.org/history/view?id=d88c1ef77619eb4f ----------------------------------------------------------------------------- The user 'bsib@leeds.ac.uk' provided the following information:
Same as before but the reference genome is UCSC MAin on Human:refFlat ----------------------------------------------------------------------------- job id: 6096851 tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6 job pid or drm id: 136948 ----------------------------------------------------------------------------- job command line: python /galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/b01956f26c36/cufflinks/cufflinks_wrapper.py --input=/galaxy-repl/main/files/007/074/dataset_7074022.dat --assembled-isoforms-output=/galaxy-repl/main/files/007/081/dataset_7081835.dat --num-threads="8" -I 300000 -F 0.1 -j 0.15 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -N -b --ref_file="None" --dbkey=hg18 --index_dir=/galaxy/main/server/tool-data -u ----------------------------------------------------------------------------- job stderr: Error running cufflinks. return code = 1 Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa /galaxy-repl/main/files/007/074/dataset_7074022.dat Error: cannot open reference GTF file /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat for reading
----------------------------------------------------------------------------- job stdout: cufflinks v2.1.1 cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). -- Jennifer Hillman-Jackson http://galaxyproject.org
-- Jennifer Hillman-Jackson http://galaxyproject.org
Hello Irene, Are you using the public Main Galaxy instance at http://usegalaxy.org? And the tool "Get Data -> Upload File"? Following these instructions (there is a video): http://wiki.galaxyproject.org/Support#Loading_data Typing "human" in the " Genome:" box should bring up the hg* choices. Please check and let us know. Jen Galaxy team On 11/27/13 2:53 PM, Irene Bassano wrote:
Hi Jen, thanks.
I am a bit confused: on Galaxy the only human genome listed is hg_g1k_v37.
So when I uploaded the new data from "Get data", under "Genome" I selected hg_g1k_v37
Now, all i want is to get cufflinks with gene names: which genome am I supposed to use? the only one I knew was hg19 from iGenomes...but seems i cannot use it. Do I have to select a genome when I upload raw fastq data? I havent stated doign anything so far, its just raw data
Thanks a lot, Irene ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Wednesday, November 27, 2013 10:08 PM To: Irene Bassano Cc: galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk
Hello,
iGenomes covers the UCSC build, and this named "Human Feb. 2009 (GRCh37/hg19) (hg19)" in the full name in the UI. The "hg19" key is the important part - as the name may be abbreviated in some tools, but this key will be in all. The genome with the "hg_g1k_v37" key is slightly different and you will have another genome mismatch problem with the RNA-seq (and most other) tools if you combine this genome with data from UCSC (the source of hg19) or the wrong iGenomes file.
"hg_g1k_v37" (source: 1000 genomes via GATK) and "hg19" (source: UCSC) are just about the same, but the identifiers are different. If you want to examine the differences, both are available on our rsync server and can be downloaded and compared. On the "Help -> Support" wiki are links for reference genomes.
The iGenomes GTF file for hg19 is on the public Main server, if that is more convenient for you, or should you just want to be sure you have the right one. Look in Shared Data -> Data Libraries -> iGenomes.
Best,
Jen Galaxy team
ps. please try to send new questions to one of our lists, thanks!
On 11/27/13 12:51 PM, Irene Bassano wrote:
Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list ""Homo sapiens b37(hg_g1k_v37).
Is this the same as the genome listed in UCSC "February 2009 (GRCh37/hg19)"?
I am using iGenomes to get the gene names rather than annotation such as NM_00xxxx and I fused the UCSC website choosing the newest genome, February 2009
Thanks,
best, Irene ________________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: Monday, November 18, 2013 7:26 PM To: galaxy-bugs@bx.psu.edu; Irene Bassano Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk
Hi again,
The database mismatch is a problem here is well for the same reasons. My guess is that you intended to run dataset #21 against hg19, and that the run against hg18 was a tool form input mistake?
Good luck with the next runs,
Jen Galaxy team
On 11/18/13 5:21 AM, galaxy-bugs@bx.psu.edu wrote:
GALAXY TOOL ERROR REPORT ------------------------
This error report was sent from the Galaxy instance hosted on the server "usegalaxy.org" ----------------------------------------------------------------------------- This is in reference to dataset id 7081835 from history id 1686699 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item
37: Cufflinks on data 21 and data 34: assembled transcripts
by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.
usegalaxy.org/history/view?id=d88c1ef77619eb4f ----------------------------------------------------------------------------- The user 'bsib@leeds.ac.uk' provided the following information:
Same as before but the reference genome is UCSC MAin on Human:refFlat ----------------------------------------------------------------------------- job id: 6096851 tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6 job pid or drm id: 136948 ----------------------------------------------------------------------------- job command line: python /galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/b01956f26c36/cufflinks/cufflinks_wrapper.py --input=/galaxy-repl/main/files/007/074/dataset_7074022.dat --assembled-isoforms-output=/galaxy-repl/main/files/007/081/dataset_7081835.dat --num-threads="8" -I 300000 -F 0.1 -j 0.15 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -N -b --ref_file="None" --dbkey=hg18 --index_dir=/galaxy/main/server/tool-data -u ----------------------------------------------------------------------------- job stderr: Error running cufflinks. return code = 1 Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa /galaxy-repl/main/files/007/074/dataset_7074022.dat Error: cannot open reference GTF file /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat for reading
----------------------------------------------------------------------------- job stdout: cufflinks v2.1.1 cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). -- Jennifer Hillman-Jackson http://galaxyproject.org
-- Jennifer Hillman-Jackson http://galaxyproject.org
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-- Jennifer Hillman-Jackson http://galaxyproject.org
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Irene Bassano -
Jennifer Jackson