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Old 07-01-2011, 11:35 AM   #1
townway
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Location: Rockville

Join Date: May 2009
Posts: 40
Default cuffmerge-*.tmap missing

I am running cuffmerge to combine some of samples GTF files. And error is showing as follow. Would you please tell me what I should do to fix the problem? Thank you so much!


$ /usr/local/cufflinks/bin/cuffmerge -s /reference/hg19.fasta assembly_GTF_list.txt.txt

[Fri Jul 1 11:33:03 2011] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Jul 1 11:33:03 2011] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Fri Jul 1 11:33:03 2011] Converting GTF files to SAM
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[11:33:03] Loading reference annotation.
[Fri Jul 1 11:33:03 2011] Assembling transcripts
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
[bam_header_read] EOF marker is absent.
File ./merged_asm/tmp/mergeSam_fileaw7mto doesn't appear to be a valid BAM file, trying SAM...
[11:33:03] Inspecting reads and determining fragment length distribution.
Processed 121 loci. > Map Properties:
> Total Map Mass: 968.00
> Read Type: 173bp single-end
> Fragment Length Distribution: Gaussian (default)
> Estimated Mean: 246.97
> Estimated Std Dev: 52.49
[11:33:03] Assembling transcripts and estimating abundances.
Processed 121 loci. [Fri Jul 1 11:33:05 2011] Comparing against reference file None
Traceback (most recent call last):
File "/usr/local/cufflinks/bin/cuffmerge", line 573, in ?
sys.exit(main())
File "/usr/local/cufflinks/bin/cuffmerge", line 556, in main
compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
File "/usr/local/cufflinks/bin/cuffmerge", line 410, in compare_meta_asm_against_ref
f_tmap = open(tmap)
IOError: [Errno 2] No such file or directory: './merged_asm/tmp_meta_asm.transcripts.gtf.tmap'
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