Re: [galaxy-user] Running Cufflinks on Bacterial RNAseq data
Peter is correct (I oversimplified)! And Cufflinks does allow for an ID attribute to span lines as long as it represents the same feature. To be clear, this error was a true format issue. The best way to understand the finer points is to see the specification (also linked from wiki below): http://www.sequenceontology.org/gff3.shtml (quote) Column 9: "attributes" <...> ID Indicates the ID of the feature. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature. Thanks Peter for the clarification! Jen Galaxy team On 7/31/12 11:35 AM, Jennifer Jackson wrote: Hello Rachel, When datasets are in a grey "waiting to run" state this indicates that they are in the queue and in line to run. For the majority of cases, including yours, leaving the job alone and allowing it to run is the correct option. The missing metadata only means that the result has not yet posted to your history (expected when still grey). It looks as if your jobs have now run, but resulted in errors. I can let you know that the problem is with the input GFF3 dataset. It contains at least one duplicated "ID" attribute, which is required to be unique within GFF3 files. Clicking on the green bug icon in any of the red error datasets will point to the example duplicated ID. To my knowledge, the content being based on a bacterial genome is unrelated to this format problem. For reference, this is the specification help for GFF3: http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF3 This can be a difficult problem to resolve on your own since the scope of the true file issues are unknown. Locating an alternate source or contacting the original source of this GFF3 dataset to request a correction would be potential solutions. The tophat.cuffli...@gmail.com mailing list or seqanswers.com are suggested places to query for reference annotation file recommendations. Best, Jen Galaxy team On 7/27/12 10:30 AM, Rachel Krasich wrote: I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks. Rachel ___ 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/
Re: [galaxy-user] Running Cufflinks on Bacterial RNAseq data
On Tue, Jul 31, 2012 at 7:35 PM, Jennifer Jackson wrote: > Hello Rachel, > > When datasets are in a grey "waiting to run" state this indicates that they > are in the queue and in line to run. For the majority of cases, including > yours, leaving the job alone and allowing it to run is the correct option. > The missing metadata only means that the result has not yet posted to your > history (expected when still grey). > > It looks as if your jobs have now run, but resulted in errors. I can let you > know that the problem is with the input GFF3 dataset. It contains at least > one duplicated "ID" attribute, which is required to be unique within GFF3 > files. Actually that isn't quite right (although it may be a limitation imposed by some tools using GFF3 as an input). Features split over multiple locations are described in GFF3 using multiple lines sharing the same ID attribute. This is most commonly used for genes made up of multiple exons, but can even apply across references in some extreme trans-splicing cases. Peter ___ 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] Running Cufflinks on Bacterial RNAseq data
Hello Rachel, When datasets are in a grey "waiting to run" state this indicates that they are in the queue and in line to run. For the majority of cases, including yours, leaving the job alone and allowing it to run is the correct option. The missing metadata only means that the result has not yet posted to your history (expected when still grey). It looks as if your jobs have now run, but resulted in errors. I can let you know that the problem is with the input GFF3 dataset. It contains at least one duplicated "ID" attribute, which is required to be unique within GFF3 files. Clicking on the green bug icon in any of the red error datasets will point to the example duplicated ID. To my knowledge, the content being based on a bacterial genome is unrelated to this format problem. For reference, this is the specification help for GFF3: http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF3 This can be a difficult problem to resolve on your own since the scope of the true file issues are unknown. Locating an alternate source or contacting the original source of this GFF3 dataset to request a correction would be potential solutions. The tophat.cuffli...@gmail.com mailing list or seqanswers.com are suggested places to query for reference annotation file recommendations. Best, Jen Galaxy team On 7/27/12 10:30 AM, Rachel Krasich wrote: I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks. Rachel ___ 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] Running Cufflinks on Bacterial RNAseq data
I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped my reads using an outside program (Genious) and uploaded the resulting BAM file. I also have uploaded the E. coli annotations as a gtf file. However when I attempt to run Cufflinks using my annotations it just stays on "Job is waiting to run" for hours. If I click on "Edit attributes", I see an error message "Required metadata values are missing". Does this mean that my files are somehow incomplete and cufflinks will never run, or do I just need to wait longer? When searching around the mailing lists I saw others have had issues with bacteria due to its circular chromosome, and was wondering if this might somehow be related. Thanks. Rachel ___ 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] Running cufflinks on a genome without a bowtie index
Noa, Using your FASTA in Tophat and Cufflinks is the correct approach. You don't need to provide an annotation file in Cufflinks, and you can also avoid using your FASTA in Cufflinks by not using bias correction. If you're still having problems, the issue is likely your parameter choices in Tophat and/or Cufflinks. You'll want to read the documentation carefully to choose parameters appropriately for your data. Good luck, J. On Dec 22, 2011, at 5:09 AM, Noa Sher wrote: > Hi > I am trying to run Cufflinks on a genome without a bowtie index. > How do I make my own index? I have a FASTA file of the genome, but if I run > tophat using just that and then cufflinks using a gtf file of the > transcriptome, I get zero in all FPKM values > Thanks > Noa > ___ > 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] Running cufflinks on a genome without a bowtie index
Hi I am trying to run Cufflinks on a genome without a bowtie index. How do I make my own index? I have a FASTA file of the genome, but if I run tophat using just that and then cufflinks using a gtf file of the transcriptome, I get zero in all FPKM values Thanks Noa ___ 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] running cufflinks
On Tue, Sep 6, 2011 at 9:29 PM, Peng, Tao wrote: > Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY > ensemble were recognized by GALAXY cufflinks as a GTF file although they > all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as > GFF files? > > Thx, I'm pretty sure Galaxy ignores the original filename extension (it will be stored on disk as *.dat once uploaded to Galaxy). If you could post the start of each file (or links to the complete files) that would be very helpful for working out why Galaxy has misidentified the GTF files as GFF. Peter ___ 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] running cufflinks
===> Please use "Reply All" when responding to this email<===
Hello,
File type can be set by using a dataset's pencil icon to reach the "Edit
Attributes" form. GTF and GFF are both very similar. It is possible that
the 9th field ("group" for GFF, "attributes" for GTF) was not detected
automatically upon upload or that there is some problem with format to
double check (extra tabs or whitespace).
Hopefully this helps,
Best,
Jen
Galaxy team
On 9/6/11 1:29 PM, Peng, Tao wrote:
> Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY
> ensemble were recognized by GALAXY cufflinks as a GTF file although they
> all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as
> GFF files?
>
> Thx,
>
> tao
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
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use the Galaxy Development list:
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Re: [galaxy-user] running cufflinks
Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY ensemble were recognized by GALAXY cufflinks as a GTF file although they all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as GFF files? Thx, tao -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, September 01, 2011 5:08 PM To: galaxy-user Cc: Peng, Tao Subject: running cufflinks ===> Please use "Reply All" when responding to this email <=== Hello, This is the same reply as for the bug report, but for others who may run into the same problem job that fails with this error: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc the reason is explained in #3 in the RNA-seq FAQ: http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq#faq3 A local or cloud instance may be the solution. These options are explained here: http://galaxyproject.org/wiki/Big%20Picture/Choices Our apologies for any inconvenience, Best, Jen Galaxy team On 9/1/11 4:55 PM, Peng, Tao wrote: > Hi I am NOT sure why running cufflinks failed here. Thanks for your > suggestion, > > tao > > --- > Tool: Cufflinks > Name: Cufflinks on data 6 and data 26: assembled transcripts > Created: Sep 01, 2011 > Filesize: 81.3 Mb > Dbkey: hg19 > Format: gtf > Tool Version: > > Input Parameter Value > SAM or BAM file of aligned RNA-Seq reads 6: Tophat for > R4_CG_wh_accepted_hits > Max Intron Length 30 > Min Isoform Fraction 0.05 > Pre MRNA Fraction 0.05 > Perform quartile normalization Yes > Conditional (reference_annotation) 1 > Reference Aonnotation 26: Homo_sapiens.GRCh37.63.gtf > Conditional (bias_correction) 0 > Conditional (seq_source) 0 > Conditional (singlePaired) 0 > > -- > > Message from History panel in GALAXY: > > An error occurred running this job: cufflinks v1.0.3 > cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -N > -b /galaxy/data/hg19/sam_index/hg19.fa > Error running cufflinks. [18:40:45] Inspecting reads and determining > fragment length distribution. > Processed 915556 loci. > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/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/
[galaxy-user] running cufflinks
Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion, tao --- Tool: Cufflinks Name: Cufflinks on data 6 and data 26: assembled transcripts Created:Sep 01, 2011 Filesize: 81.3 Mb Dbkey: hg19 Format: gtf Tool Version: Input Parameter Value SAM or BAM file of aligned RNA-Seq reads6: Tophat for R4_CG_wh_accepted_hits Max Intron Length 30 Min Isoform Fraction0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Aonnotation 26: Homo_sapiens.GRCh37.63.gtf Conditional (bias_correction) 0 Conditional (seq_source)0 Conditional (singlePaired) 0 -- Message from History panel in GALAXY: An error occurred running this job: cufflinks v1.0.3 cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -N -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [18:40:45] Inspecting reads and determining fragment length distribution. Processed 915556 loci. ___ 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] running cufflinks
===> Please use "Reply All" when responding to this email <=== Hello, This is the same reply as for the bug report, but for others who may run into the same problem job that fails with this error: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc the reason is explained in #3 in the RNA-seq FAQ: http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq#faq3 A local or cloud instance may be the solution. These options are explained here: http://galaxyproject.org/wiki/Big%20Picture/Choices Our apologies for any inconvenience, Best, Jen Galaxy team On 9/1/11 4:55 PM, Peng, Tao wrote: Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion, tao --- Tool: Cufflinks Name: Cufflinks on data 6 and data 26: assembled transcripts Created: Sep 01, 2011 Filesize: 81.3 Mb Dbkey: hg19 Format: gtf Tool Version: Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 6: Tophat for R4_CG_wh_accepted_hits Max Intron Length 30 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Aonnotation 26: Homo_sapiens.GRCh37.63.gtf Conditional (bias_correction) 0 Conditional (seq_source) 0 Conditional (singlePaired) 0 -- Message from History panel in GALAXY: An error occurred running this job: cufflinks v1.0.3 cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -N -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [18:40:45] Inspecting reads and determining fragment length distribution. Processed 915556 loci. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/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/
