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:[email protected]] 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 300000 > 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 300000 -F 0.050000 -j 0.050000 -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/
