Running Cufflinks

Question: Running Cufflinks

7.2 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

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modified 9 months ago by hamid_fiuji • 0 • written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k

7.2 years ago by

Peng, Tao • 170

Peng, Tao • 170 wrote:

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

ADD COMMENT • link written 7.2 years ago by Peng, Tao • 170

I'm pretty sure Galaxy ignores the original filename extension (it will be stored on disk as *.dat once uploaded to Galaxy). If you could post the start of each file (or links to the complete files) that would be very helpful for working out why Galaxy has misidentified the GTF files as GFF. Peter

ADD REPLY • link written 7.2 years ago by Peter Cock • 1.4k

hello i am using tuxedo tools on the Ubuntu and i have a problem with my cuffdiff . it gives an error entitled "what(): std::bad_alloc" at the end of process. is there any one help me how i can tackle this problem in ubunto. i am not perfect in using linux and i need a person patiently show me the ways at the easiest way. thank you very much. my email contact is "hamid_fiuji@yahoo.com"

ADD REPLY • link written 9 months ago by hamid_fiuji • 0

9 months ago by

hamid_fiuji • 0

hamid_fiuji • 0 wrote:

i have a problem with my cuffdiff . it gives an error entitled "what(): std::bad_alloc" at the end of process. is there any one help me how i can tackle this problem in ubunto. i am not perfect in using linux and i need a person patiently show the solution at the easiest way. thank you very much. my email contact is "hamid_fiuji@yahoo.com"

ADD COMMENT • link written 9 months ago by hamid_fiuji • 0

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