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?



-----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 <===


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
> 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
> -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

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