Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from m.p.villerius@lumc.nl
Michel, The newest versions of SAM Tools are on our main public server now. If you could try again, that would be helpful. If it does fail again, please do share your history with me (kpvincent@bx.psu.edu). Otherwise, it's good that you were able to get it working locally. The error suppression is actually what we just dealt with with the latest version of the tools. Now it should capture the stderr and output it only if it was an actual error, instead of disrupting successful runs. Galaxy doesn't have any special PATH settings. You just need to make sure that the binary is available on your PATH environment variable when you run Galaxy. Out of the SAM Tools heading tools, only Merge BAM Files and Generate pileup actually rely on the samtools binary, so maybe that's why it seemed like the others were working. I'm not sure on your last question and will forward it to our list for someone else to answer. Regards, Kelly On Thu 25 Feb 2010, at 3:46 AM, vill wrote:
Hi Kelly,
Yes I tried both places. The test.galaxy server is slow or not responding right now. 25 Feb. 9:10 am Amsterdam time thus I can't test samtools there. The error I got on my local install is solved, I removed in the sam_to_bam.py the following "2> /dev/null" and the error was can't find the path. I copied samtools to the /usr/local/bin dir and now everything is working. Strange because the other samtools seemed to work. How do I add a extra PATH to GALAXY?
It won't be any problem sharing my History if you need it.
One other thing when we get data from UCSC main, the data will become a history item. When you look at this history item in the info: there used to be a link so you could view the data in the UCSC browser: Info: UCSC Main on Human: The txt is there but it is not a link, is this something we need to add in the configuration?
//Michel
On Wed, 2010-02-24 at 10:38 -0500, Kelly Vincent wrote:
Michel,
Your other email indicated that you are running a local instance of Galaxy, but this error report is from our public server, so I'm assuming you tried it both places. Our SAM Tools wrappers have recently been slightly rewritten, in changeset 3426:1f05b0c4071f, although the changed versions haven't been uploaded to the public server yet. You should try rerunning the job with the new version (it should be providing more information when something fails). If you want to try it on main, I can let you know once it's been updated. Also, the new version is already on our test server (http://test.g2.bx.psu.edu/ ) if you want to try right away without upgrading your local install. If you try it on test and it fails, could you share your history with me (kpvincent@bx.psu.edu)?
Thanks, Kelly
On Mon 22 Feb 2010, at 8:40 AM, galaxy-bugs@bx.psu.edu wrote:
GALAXY TOOL ERROR REPORT ------------------------
This error report was sent from the Galaxy instance hosted on the server "main.g2.bx.psu.edu" ----------------------------------------------------------------------------- This is in reference to dataset id 1078127 from history id 322475 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item
4: SAM-to-BAM on data 3 and data 2
by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.
main.g2.bx.psu.edu/history/view?id=e9709e1ba7514892 ----------------------------------------------------------------------------- The user 'm.p.villerius@lumc.nl' provided the following information:
Uploaded a .sam file, uploaded my reference file and tried a sam to bam conversion. I also have an other error on my local Galaxy install -> ################### Traceback (most recent call last): File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line 113, in if __name__=="__main__": __main__() File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line 103, in __main__ shutil.move( sorted_bam_file, options.output1 ) File "/usr/lib/python2.6/shutil.py", line 264, in move copy2(src, real_dst) File "/usr/lib/python2.6/shutil.py", line 99, in copy2 copyfile(src, dst) File "/usr/lib/python2.6/shutil.py", line 52, in copyfile fsrc = open(src, 'rb') IOError: [Errno 2] No such file or directory: '/tmp/381.1.all.q/ tmpJzAOLW.bam' ###################### Same file and reference? All works fine on command line. ----------------------------------------------------------------------------- job id: 855615 tool id: sam_to_bam ----------------------------------------------------------------------------- job command line: python /galaxy/home/g2main/galaxy_main/tools/samtools/sam_to_bam.py --input1=/galaxy/home/g2main/galaxy_main/database/files/001/078/ dataset_1078112.dat --dbkey=? --ref_file=/galaxy/home/g2main/ galaxy_main/database/files/001/078/dataset_1078114.dat --output1=/ galaxy/home/g2main/galaxy_main/database/tmp/job_working_directory/ 855615/galaxy_dataset_1078127.dat --index_dir=/galaxy/home/g2main/ galaxy_main/tool-data ----------------------------------------------------------------------------- job stderr: /bin/sh: line 1: 20580 Segmentation fault samtools view -bt / space/g2main/dataset_1078114.dat -o /space/g2main/tmpM7xmZe /galaxy/ home/g2main/galaxy_main/database/files/001/078/dataset_1078112.dat 2> /dev/null /bin/sh: line 1: 20583 Aborted samtools sort /space/ g2main/tmpM7xmZe /space/g2main/tmpmvKLRC 2> /dev/null Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/samtools/ sam_to_bam.py", line 113, in <module> if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/samtools/ sam_to_bam.py", line 103, in __main__ shutil.move( sorted_bam_file, options.output1 ) File "/usr/lib/python2.5/shutil.py", line 199, in move copy2(src,dst) File "/usr/lib/python2.5/shutil.py", line 91, in copy2 copyfile(src, dst) File "/usr/lib/python2.5/shutil.py", line 46, in copyfile fsrc = open(src, 'rb') IOError: [Errno 2] No such file or directory: '/space/g2main/ tmpmvKLRC.bam'
----------------------------------------------------------------------------- job stdout:
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). _______________________________________________ galaxy-bugs mailing list galaxy-bugs@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-bugs
Kelly, I can confirm that my dataset is working now on the test instance. Thanks, the next step in the analysis is Varscan on the pileup file. I have this on my local install and that works. Thanks team for creating Galaxy. //Michel On Thu, 2010-02-25 at 11:15 -0500, Kelly Vincent wrote:
Michel,
The newest versions of SAM Tools are on our main public server now. If you could try again, that would be helpful. If it does fail again, please do share your history with me (kpvincent@bx.psu.edu).
Otherwise, it's good that you were able to get it working locally. The error suppression is actually what we just dealt with with the latest version of the tools. Now it should capture the stderr and output it only if it was an actual error, instead of disrupting successful runs.
Galaxy doesn't have any special PATH settings. You just need to make sure that the binary is available on your PATH environment variable when you run Galaxy. Out of the SAM Tools heading tools, only Merge BAM Files and Generate pileup actually rely on the samtools binary, so maybe that's why it seemed like the others were working.
I'm not sure on your last question and will forward it to our list for someone else to answer.
Regards, Kelly
On Thu 25 Feb 2010, at 3:46 AM, vill wrote:
Hi Kelly,
Yes I tried both places. The test.galaxy server is slow or not responding right now. 25 Feb. 9:10 am Amsterdam time thus I can't test samtools there. The error I got on my local install is solved, I removed in the sam_to_bam.py the following "2> /dev/null" and the error was can't find the path. I copied samtools to the /usr/local/bin dir and now everything is working. Strange because the other samtools seemed to work. How do I add a extra PATH to GALAXY?
It won't be any problem sharing my History if you need it.
One other thing when we get data from UCSC main, the data will become a history item. When you look at this history item in the info: there used to be a link so you could view the data in the UCSC browser: Info: UCSC Main on Human: The txt is there but it is not a link, is this something we need to add in the configuration?
//Michel
On Wed, 2010-02-24 at 10:38 -0500, Kelly Vincent wrote:
Michel,
Your other email indicated that you are running a local instance of Galaxy, but this error report is from our public server, so I'm assuming you tried it both places. Our SAM Tools wrappers have recently been slightly rewritten, in changeset 3426:1f05b0c4071f, although the changed versions haven't been uploaded to the public server yet. You should try rerunning the job with the new version (it should be providing more information when something fails). If you want to try it on main, I can let you know once it's been updated. Also, the new version is already on our test server (http://test.g2.bx.psu.edu/ ) if you want to try right away without upgrading your local install. If you try it on test and it fails, could you share your history with me (kpvincent@bx.psu.edu)?
Thanks, Kelly
On Mon 22 Feb 2010, at 8:40 AM, galaxy-bugs@bx.psu.edu wrote:
GALAXY TOOL ERROR REPORT ------------------------
This error report was sent from the Galaxy instance hosted on the server "main.g2.bx.psu.edu" ----------------------------------------------------------------------------- This is in reference to dataset id 1078127 from history id 322475 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item
4: SAM-to-BAM on data 3 and data 2
by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link.
main.g2.bx.psu.edu/history/view?id=e9709e1ba7514892 ----------------------------------------------------------------------------- The user 'm.p.villerius@lumc.nl' provided the following information:
Uploaded a .sam file, uploaded my reference file and tried a sam to bam conversion. I also have an other error on my local Galaxy install -> ################### Traceback (most recent call last): File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line 113, in if __name__=="__main__": __main__() File "/usr/local/galaxy_dist/tools/samtools/sam_to_bam.py", line 103, in __main__ shutil.move( sorted_bam_file, options.output1 ) File "/usr/lib/python2.6/shutil.py", line 264, in move copy2(src, real_dst) File "/usr/lib/python2.6/shutil.py", line 99, in copy2 copyfile(src, dst) File "/usr/lib/python2.6/shutil.py", line 52, in copyfile fsrc = open(src, 'rb') IOError: [Errno 2] No such file or directory: '/tmp/381.1.all.q/ tmpJzAOLW.bam' ###################### Same file and reference? All works fine on command line. ----------------------------------------------------------------------------- job id: 855615 tool id: sam_to_bam ----------------------------------------------------------------------------- job command line: python /galaxy/home/g2main/galaxy_main/tools/samtools/sam_to_bam.py --input1=/galaxy/home/g2main/galaxy_main/database/files/001/078/ dataset_1078112.dat --dbkey=? --ref_file=/galaxy/home/g2main/ galaxy_main/database/files/001/078/dataset_1078114.dat --output1=/ galaxy/home/g2main/galaxy_main/database/tmp/job_working_directory/ 855615/galaxy_dataset_1078127.dat --index_dir=/galaxy/home/g2main/ galaxy_main/tool-data ----------------------------------------------------------------------------- job stderr: /bin/sh: line 1: 20580 Segmentation fault samtools view -bt / space/g2main/dataset_1078114.dat -o /space/g2main/tmpM7xmZe /galaxy/ home/g2main/galaxy_main/database/files/001/078/dataset_1078112.dat 2> /dev/null /bin/sh: line 1: 20583 Aborted samtools sort /space/ g2main/tmpM7xmZe /space/g2main/tmpmvKLRC 2> /dev/null Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/samtools/ sam_to_bam.py", line 113, in <module> if __name__=="__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/samtools/ sam_to_bam.py", line 103, in __main__ shutil.move( sorted_bam_file, options.output1 ) File "/usr/lib/python2.5/shutil.py", line 199, in move copy2(src,dst) File "/usr/lib/python2.5/shutil.py", line 91, in copy2 copyfile(src, dst) File "/usr/lib/python2.5/shutil.py", line 46, in copyfile fsrc = open(src, 'rb') IOError: [Errno 2] No such file or directory: '/space/g2main/ tmpmvKLRC.bam'
----------------------------------------------------------------------------- job stdout:
----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message). _______________________________________________ galaxy-bugs mailing list galaxy-bugs@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-bugs
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