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
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
