===> Please use "Reply All" when responding to this email <===


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:

A local or cloud instance may be the solution. These options are explained here:

Our apologies for any inconvenience,


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


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
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
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:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to