[galaxy-user] Cuffdiff errors
Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using Galaxy through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19. Here's the error: An error occurred running this job: *cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.05 -b /galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g* Thanks for the help. -- Erin Shanle Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 sha...@wisc.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Trackster errors
Hello I would like to visualize the tracks of my tophat accepted hits bam file. I ran my first sample that was ~10,000,000 reads and it could be visualized in both Trackster and the UCSC genome browser. When I tried to visualize my other samples (which ranged from 15,000,000 to 35,000,000 reads) it won't show up in trackster because of an indexing error. When I ran Picard statistics on the tophat accepted hits bam output, I see that there was successful alignment of ~90% of the reads. Since I have one sample that works, I am not sure how to address the issue. Here's the error I get from Trackster when I try to visualize the samples: *** glibc detected *** python: double free or corruption (!prev): 0x00ff02b0 *** === Backtrace: = /lib/libc.so.6(+0x71ad6)[0x7ff6561f7ad6] /lib/libc.so.6(cfree+0x6c)[0x7ff6561fc84c] /lib/libc.so.6(fclose+0x14d)[0x7ff6561e8a1d] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7ff655cdbb17] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x6e838)[0x7ff655cc7838] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_CallObjectWithKeywords+0x43)[0x4a1a53] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x52a44)[0x7ff655caba44] python[0x46f0a3] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_EvalFrameEx+0x4878)[0x4a72b8] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalFrameEx+0x4d12)[0x4a7752] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalCode+0x32)[0x4a9692] python(PyRun_FileExFlags+0x13e)[0x4c98be] python(PyRun_SimpleFileExFlags+0xd4)[0x4c9ad4] python(Py_Main+0x9ed)[0x41a6bd] /lib/libc.so.6(__libc_start_main+0xfd)[0x7ff6561a4c4d] python[0x4198d9] === Memory map: 0040-0061d000 r-xp fe:00 715090 /usr/bin/python2.6 0081d000-0087f000 rw-p 0021d000 fe:00 715090 /usr/bin/python2.6 0087f000-0088e000 rw-p 00:00 0 00d1a000-0109a000 rw-p 00:00 0 [heap] 7ff65000-7ff650021000 rw-p 00:00 0 7ff650021000-7ff65400 ---p 00:00 0 7ff6556ed000-7ff655702000 r-xp fe:00 1512749 /lib/libgcc_s.so.1 7ff655702000-7ff655902000 ---p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655902000-7ff655903000 rw-p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655903000-7ff655933000 r-xp 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655933000-7ff655a32000 ---p 0003 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a32000-7ff655a37000 rw-p 0002f000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a37000-7ff655a39000 rw-p 00:00 0 7ff655a39000-7ff655a55000 r-xp fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655a55000-7ff655c55000 ---p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c55000-7ff655c59000 rw-p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c59000-7ff655d29000 r-xp 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655d29000-7ff655e29000 ---p 000d 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e29000-7ff655e39000 rw-p 000d 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e39000-7ff655ec rw-p 00:00 0 7ff655fc-7ff656185000 rw-p 00:00 0 7ff656186000-7ff6562de000 r-xp fe:00 1514734 /lib/libc-2.11.2.so 7ff6562de000-7ff6564dd000 ---p 00158000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564dd000-7ff6564e1000 r--p 00157000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564e1000-7ff6564e2000 rw-p 0015b000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564e2000-7ff6564e7000 rw-p 00:00 0 7ff6564e7000-7ff656567000 r-xp fe:00 1514738 /lib/libm-2.11.2.so 7ff656567000-7ff656767000 ---p 0008 fe:00 1514738 /lib/libm-2.11.2.so 7ff656767000-7ff656768000 r--p 0008 fe:00 1514738 /lib/libm-2.11.2.so 7ff656768000-7ff656769000 rw-p 00081000 fe:00 1514738 /lib/libm-2.11.2.so 7ff656769000-7ff65678 r-xp fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff65678-7ff65697f000 ---p 00017000 fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff65697f000-7ff65698 rw-p 00016000 fe:00 713314 /usr/lib/libz.so.1.2.3.4 7ff65698-7ff656af5000 r-xp fe:00 713850 /usr/lib/libcrypto.so.0.9.8 7ff656af5000-7ff656cf5000 ---p 00175000 fe:00 713850 /usr/lib/libcrypto.so.0.9.8 7ff656cf5000-7ff656d1d000 rw-p
[galaxy-user] January 20, 2012 Galaxy Development News Brief
January 20, 2012 Galaxy Development News Brief Highlights: * New Object Store data integration layer introduced * RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, CuffCompare to 1.3.0. * Tool Shed installation features and community tool additions * Trackster performance upgrades and new drag drop composite track creation Mercurial pull: hg pull -u -r 63bc46cc73b7 Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_20 Release history http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Install/Administration Help http://getgalaxy.org Support http://galaxyproject.org/wiki/Support Thanks for using Galaxy! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Looking for an easy load test for Galaxy Cloudman
Hi Greg, We have a tutorial workflow from one of our publications that would be a good test case to use: http://usegalaxy.org/heteroplasmy It contains complete references and the text walks through from start to end and includes expected results. The Shared Workflows area on Galaxy main would also be a good resource, if more examples are needed. Best, Jen Galaxy team On 12/26/11 1:56 PM, Greg Edwards wrote: Hi, I'm experimenting with Galaxy Cloudman, and could use a simple workflow to a) test that Galaxy is working ok b) put some significant load on a Galaxy server so that it shows in the load diagram, ie. as below load.png Suggestions appreciated. Thanks, -- Greg Edwards gedwar...@gmail.com mailto:gedwar...@gmail.com ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Cuffdiff errors
Hello Erin, This was a temporary problem due to a new filesystem we installed during this time frame, that has since been resolved. Please try again and if the problem persists, please send a bug report from the error dataset using the green bug icon. This allows us to gain access to the inputs and job parameters to diagnose the root cause of the problem. http://wiki.g2.bx.psu.edu/Support#Error_from_tools http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Thank you! Jen Galaxy team On 1/20/12 6:51 AM, Erin Shanle wrote: Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my conditions. I successfully used Cuffdiff three days ago to compare two sets of data that are processed the exact same way (align with Tophat and use Picard to confirm adequate alignment). I am using Galaxy through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19. Here's the error: An error occurred running this job: /cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.05 -b /galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g/ Thanks for the help. -- Erin Shanle Graduate Research Assistant Molecular and Environmental Toxicology 425 McArdle Laboratory for Cancer Research 1400 University Ave Madison, WI 53706 608 262 9834 sha...@wisc.edu mailto:sha...@wisc.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Trackster errors
Erin, This was due to a temporary issue that has been fixed. However, you'll need to copy the problematic datasets and use the new copy for visualization. To copy datasets, use History Options -- Copy Datasets; you can select the source history as your target history to copy datasets within a history. Thanks, J. On Jan 20, 2012, at 9:57 AM, Erin Shanle wrote: Hello I would like to visualize the tracks of my tophat accepted hits bam file. I ran my first sample that was ~10,000,000 reads and it could be visualized in both Trackster and the UCSC genome browser. When I tried to visualize my other samples (which ranged from 15,000,000 to 35,000,000 reads) it won't show up in trackster because of an indexing error. When I ran Picard statistics on the tophat accepted hits bam output, I see that there was successful alignment of ~90% of the reads. Since I have one sample that works, I am not sure how to address the issue. Here's the error I get from Trackster when I try to visualize the samples: *** glibc detected *** python: double free or corruption (!prev): 0x00ff02b0 *** === Backtrace: = /lib/libc.so.6(+0x71ad6)[0x7ff6561f7ad6] /lib/libc.so.6(cfree+0x6c)[0x7ff6561fc84c] /lib/libc.so.6(fclose+0x14d)[0x7ff6561e8a1d] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7ff655cdbb17] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x6e838)[0x7ff655cc7838] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_CallObjectWithKeywords+0x43)[0x4a1a53] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so(+0x52a44)[0x7ff655caba44] python[0x46f0a3] python(PyObject_Call+0x47)[0x41ef47] python(PyEval_EvalFrameEx+0x4878)[0x4a72b8] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalFrameEx+0x4d12)[0x4a7752] python(PyEval_EvalCodeEx+0x911)[0x4a95c1] python(PyEval_EvalCode+0x32)[0x4a9692] python(PyRun_FileExFlags+0x13e)[0x4c98be] python(PyRun_SimpleFileExFlags+0xd4)[0x4c9ad4] python(Py_Main+0x9ed)[0x41a6bd] /lib/libc.so.6(__libc_start_main+0xfd)[0x7ff6561a4c4d] python[0x4198d9] === Memory map: 0040-0061d000 r-xp fe:00 715090 /usr/bin/python2.6 0081d000-0087f000 rw-p 0021d000 fe:00 715090 /usr/bin/python2.6 0087f000-0088e000 rw-p 00:00 0 00d1a000-0109a000 rw-p 00:00 0 [heap] 7ff65000-7ff650021000 rw-p 00:00 0 7ff650021000-7ff65400 ---p 00:00 0 7ff6556ed000-7ff655702000 r-xp fe:00 1512749 /lib/libgcc_s.so.1 7ff655702000-7ff655902000 ---p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655902000-7ff655903000 rw-p 00015000 fe:00 1512749 /lib/libgcc_s.so.1 7ff655903000-7ff655933000 r-xp 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655933000-7ff655a32000 ---p 0003 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a32000-7ff655a37000 rw-p 0002f000 00:13 1154848 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/ctabix.so 7ff655a37000-7ff655a39000 rw-p 00:00 0 7ff655a39000-7ff655a55000 r-xp fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655a55000-7ff655c55000 ---p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c55000-7ff655c59000 rw-p 0001c000 fe:00 738300 /usr/lib/python2.6/lib-dynload/_ctypes.so 7ff655c59000-7ff655d29000 r-xp 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655d29000-7ff655e29000 ---p 000d 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e29000-7ff655e39000 rw-p 000d 00:13 1154847 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/csamtools.so 7ff655e39000-7ff655ec rw-p 00:00 0 7ff655fc-7ff656185000 rw-p 00:00 0 7ff656186000-7ff6562de000 r-xp fe:00 1514734 /lib/libc-2.11.2.so 7ff6562de000-7ff6564dd000 ---p 00158000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564dd000-7ff6564e1000 r--p 00157000 fe:00 1514734 /lib/libc-2.11.2.so 7ff6564e1000-7ff6564e2000 rw-p 0015b000 fe:00 1514734
Re: [galaxy-user] Could you please add Vibrio cholerae O1 biovar eltor str. N16961 to the reference genome？
Hello Tao, This genome is labeled in Galaxy as: Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) However, I am guessing that the genome is not indexed for the tools you want to use it with. This means that you will need to use it as a custom reference genome. The first step is to obtain a fasta version of the genome (from either Genbank or UCSC), then upload it into your working history using FTP, and finally to use the dataset as a custom reference genome with tools (option is usually called using a reference from the history on tool form). FTP help: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP To contact UCSC about microbial genome source data downloads (Galaxy does not maintain a genome source data service), please see the contact information for the Lowe lab on the UCSC Microbial browser home page (credits section) at http://microbes.ucsc.edu/. Best wishes for your project, Jen Galaxy team On 1/19/12 7:17 AM, Tao Dong wrote: Browser Chrom/Plasmid Name Length (bp) GC Content (%) Gene Count NCBI RefSeq Accession chrI http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1position=chrI:1-2961149 2961149 47.69 2888NC_002505 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002505 chrII http://microbes.ucsc.edu/cgi-bin/hgTracks?db=vibrChol1position=chrII:1-1072315 1072315 46.91 1119NC_002506 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_002506 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
