Cuffmerge Error Allocating Memory

AsoBioInfo · 05-27-2012, 09:47 PM

Hi,

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:
SAMPLE1/transcripts.gtf
SAMPLE2/transcripts.gtf

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 (http://cufflinks.cbcb.umd.edu).
Error allocating memory.
[FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
File "./cuffmerge", line 576, in ?
sys.exit(main())
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
exit(1)
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!
Aso

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05-27-2012, 09:47 PM	#1
AsoBioInfo Member Location: KSA Join Date: Dec 2011 Posts: 37	Cuffmerge Error Allocating Memory Hi, 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: SAMPLE1/transcripts.gtf SAMPLE2/transcripts.gtf 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 (http://cufflinks.cbcb.umd.edu). Error allocating memory. [FAILED] Error: could not execute cuffcompare Traceback (most recent call last): File "./cuffmerge", line 576, in ? sys.exit(main()) 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 exit(1) 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! Aso