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:jen@bx.psu.edu] Sent: Thursday, September 01, 2011 5:08 PM To: galaxy-user Cc: Peng, Tao Subject: running cufflinks
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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.