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Old 05-27-2012, 09:47 PM   #1
Location: KSA

Join Date: Dec 2011
Posts: 37
Default Cuffmerge Error Allocating Memory


I am encountering error during Cuffmerge execution. The command I executed is:

./cuffmerge -s /extdata1/soft/TOPHAT2/hg19.fa -g UCSC-Ensembl.gtf assemblies.txt

Assemblies.txt contains two lines:

After running it gave me this error:

[15:16:59] Assembling transcripts and estimating abundances.

chr21:38435145-45747259 Warning: Skipping large bundle.
Processed 33389 loci.
[Sun May 27 16:57:47 2012] Comparing against reference file UCSC-Ensembl.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (
Error allocating memory.

Error: could not execute cuffcompare
Traceback (most recent call last):
File "./cuffmerge", line 576, in ?
File "./cuffmerge", line 559, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "./cuffmerge", line 406, in compare_meta_asm_against_ref
tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
File "./cuffmerge", line 342, in compare_to_reference
TypeError: 'str' object is not callable

It also gave me many warnings regarding the version of cufflinks (I think, It is ignorable).

I have enough memory in the server, I don't know why it is giving me this memory error. I am running two more processes of Tophat alternatively. Is that the reason it gave me this error?

Thanking you!
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