Re: [galaxy-user] Cufflinks error with illumina igenome .GTF for annnotation
Hello Sarah, This specific error code has been seen before from Cuffdiff when there is a format problem with the GTF file. A few things to double check: 1) That you downloaded the iGenomes .tar archive to your local computer or server, unpacked it using a utility or on the command line (tar -xvf), then uploaded *only* the .gtf annotation file to Galaxy? The Galaxy datatype is .gtf and there are no metadata problems (these usually show up as warnings within a yellow box, in dataset or on "Edit Attributes" form (click on pencil icon for dataset). This particular archive is known is give a few problems (various warnings due to age of software used to create archive and not all data is usable) while unpacking, but the .gtf data is intact and is small enough to load through a direct browser upload. (FTP is not needed, but you could use FTP if you wanted). If you needed to use FTP because of the data size, or you loaded via a URL directly from the source, then you very likely loaded the .tar archive itself and will need to start over: download .tar, unpack, and load just the .gtf data. 2) When you uploaded the .gtf file to Galaxy, you *did not check* the box next to "Convert spaces to tabs:". The original and upload .gtf file should have nine, tab-delimited, columns of data. If you have 12 columns, then this means the box was checked and the format is incorrect. You will want to reload the .gtf dataset (without converting spaces to tabs), after loading confirm GTF format is correct and assigned, and re-run cuffdiff. If you have any problems or are unsure about how your data fits with these checks, please submit a bug report directly from the failed CuffDiff run from the job as executed on the public main Galaxy instance. Be sure to leave all inputs and the error dataset undeleted in your history (undelete if necessary). Hopefully this helps! Jen Galaxy team On 6/1/12 10:27 AM, Sarah Elisabeth Ewald wrote: Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcript expression in 3 samples (no replicates, illumina single-end reads). Using the built in UCSC mm9 reference genome I can complete the analysis just fine, with the caveat that there is no annotation. When I repeat the analysis using the illumina igenome UCSC mm9 .gtf annotation file I get the following error in Cufflinks: An error occurred running this job: cufflinks v1.3.0 cufflinks -q --no-update-check -I 30 -F 0.10 -j 0.15 -p 8 -G /galaxy/main_pool/pool5/files/004/309/dataset_4309547.dat -N Error running cufflinks. return code = -11 cufflinks: /lib64/libz.so.1: no version information available I have set the identifier/build as "Mouse July 2007 (NCBI37/mm9) (mm9)" so that does not seem to be the probelem. Suggestions as to how to amend this problem OR add annotations to the already completed analysis would be terrific. Thanks! Sarah ___ 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://galaxyproject.org ___ 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] Cufflinks error with illumina igenome .GTF for annnotation
Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcript expression in 3 samples (no replicates, illumina single-end reads). Using the built in UCSC mm9 reference genome I can complete the analysis just fine, with the caveat that there is no annotation. When I repeat the analysis using the illumina igenome UCSC mm9 .gtf annotation file I get the following error in Cufflinks: An error occurred running this job: cufflinks v1.3.0 cufflinks -q --no-update-check -I 30 -F 0.10 -j 0.15 -p 8 -G /galaxy/main_pool/pool5/files/004/309/dataset_4309547.dat -N Error running cufflinks. return code = -11 cufflinks: /lib64/libz.so.1: no version information available I have set the identifier/build as "Mouse July 2007 (NCBI37/mm9) (mm9)" so that does not seem to be the probelem. Suggestions as to how to amend this problem OR add annotations to the already completed analysis would be terrific. Thanks! Sarah ___ 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] cufflinks error
Hello Jinhai YU, The error indicates that there was a problem with the BAM file/index. When you loaded the larger file into Galaxy, did you use FTP? Was it successful? Using a utility would allow you to track the progress, if you are not certain. An incomplete load could generate an error like the one you ran into. FTP help is at: http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP If the problem is confirmed to not be a data loading issue, it might be a good idea to go back to the SAM file and convert to BAM again (if the data was yours) or contact the owner/source of the BAM data and report the problem to see what they think. Apologies for the delay in reply, Best, Jen Galaxy team On 10/9/11 12:13 AM, jh yu wrote: Dear all: Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred: An error occurred running this job:/cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.05 -j 0.05 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat Error running cufflinks. [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this/ However, when I used the same parameters to analyze another file, it worked well: 19,904 lines format: gtf, database: rhodRHA1 Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.05 -j 0.05 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure? Thank you in advance. /Best wishes!/ / / / / / / /Sincerely, Jinhai YU/ / / / / / / /Jinhai YU, Ph.D Candidate/ /010-64888521 / /Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China/ / / ___ 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] cufflinks error
> > An error occurred running this job:cufflinks v1.0.3 > cufflinks -q --no-update-check -I 1 -F 0.05 -j 0.05 -p 8 -g = > /galaxy/main_database/files/002/991/dataset_2991920.dat > Error running cufflinks. [bam_header_read] EOF marker is absent. > [bam_header_read] invalid BAM binary header (this Hello, Without seeing your analysis, it's difficult to determine what the problem is. My best guess is that: (a) your SAM/BAM dataset is not compatible with Cufflinks for some reason, perhaps due to sorting? (b) your gene annotation dataset is not compatible with Cufflinks. Perhaps looking at the Cufflinks documentation will help you determine the error: http://cufflinks.cbcb.umd.edu/ If that doesn't work, you can report the problem by clicking on the bug icon next to the failed datasets. Good luck, J.___ 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] cufflinks error
Dear all: Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred: An error occurred running this job:cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.05 -j 0.05 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat Error running cufflinks. [bam_header_read] EOF marker is absent. [bam_header_read] invalid BAM binary header (this However, when I used the same parameters to analyze another file, it worked well: 19,904 lines format: gtf, database: rhodRHA1 Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 1 -F 0.05 -j 0.05 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure? Thank you in advance. Best wishes! Sincerely, Jinhai YU Jinhai YU, Ph.D Candidate 010-64888521 Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China ___ 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] Cufflinks error in galaxy
John, My best guess is that you are using bias correction but do not have the needed reference genome(s) for the builds that you want to use. See this page for instructions about setting up HTS tools; in particular, you'll need to set up the sam_fa_indices.loc file: https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup Best, J. On Jun 9, 2011, at 4:44 AM, 吳正華 wrote: > Hi galaxy dev team: > > I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis > according to Jeremy's excellent tutorial > > http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise > > however, I encountered following error messages when I was trying to execute > Cufflinks in galaxy.. > > Dataset generation errors > Dataset 121: Cufflinks on data 92: gene expression > Tool execution generated the following error message: > Error running cufflinks. [Errno 2] No such file or directory: > 'transcripts.gtf' > The tool produced the following additional output: > cufflinks v1.0.3 > cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 4 -b > > how should I solve this problem? > > Thanks in advance. > > > Best Regards, > > John Wu > > ___ > 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/ ___ 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] Cufflinks error in galaxy
Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis according to Jeremy's excellent tutorial http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise however, I encountered following error messages when I was trying to execute Cufflinks in galaxy.. Dataset generation errors Dataset 121: Cufflinks on data 92: gene expression Tool execution generated the following error message: Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' The tool produced the following additional output: cufflinks v1.0.3 cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 4 -b how should I solve this problem? Thanks in advance. Best Regards, John Wu ___ 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/
