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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.


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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