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Old 11-18-2015, 05:55 AM   #8
4galaxy7
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Location: UK

Join Date: Nov 2015
Posts: 19
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Well it comes out with this...

Code:
user@IT060209:~/Downloads/cufflinks$ cuffmerge -o /home/user/Desktop/sam/cuffmerge_out -s /home/user/Downloads/DinoAntAssembly3.fna.1.fasta /home/user/Desktop/sam/gtf_manifest.txt
[Wed Nov 18 14:53:07 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Nov 18 14:53:07 2015] Preparing output location /home/user/Desktop/sam/cuffmerge_out/
Warning: no reference GTF provided!
[Wed Nov 18 14:53:08 2015] Converting GTF files to SAM
[14:53:08] Loading reference annotation.
[14:53:09] Loading reference annotation.
[14:53:10] Loading reference annotation.
[14:53:10] Loading reference annotation.
[14:53:11] Loading reference annotation.
[14:53:12] Loading reference annotation.
[14:53:12] Loading reference annotation.
[14:53:13] Loading reference annotation.
[14:53:13] Loading reference annotation.
[14:53:14] Loading reference annotation.
[14:53:14] Loading reference annotation.
[14:53:15] Loading reference annotation.
[Wed Nov 18 14:53:16 2015] Assembling transcripts
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o /home/user/Desktop/sam/cuffmerge_out/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 /home/user/Desktop/sam/cuffmerge_out/tmp/mergeSam_fileil7A8s 
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /home/user/Desktop/sam/cuffmerge_out/tmp/mergeSam_fileil7A8s doesn't appear to be a valid BAM file, trying SAM...
[14:53:16] Inspecting reads and determining fragment length distribution.
Processed 10522 loci.                       
> Map Properties:
>	Normalized Map Mass: 286548.00
>	Raw Map Mass: 286548.00
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[14:53:18] Assembling transcripts and estimating abundances.
Processed 10548 loci.                       
[Wed Nov 18 14:54:34 2015] Comparing against reference file None
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
[Wed Nov 18 14:54:39 2015] Comparing against reference file None
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
It produces a seemingly OK merged file, but given that it had several errors/warnings, I'd quite like to use it with the most up to date version of cuffmerge to make sure there's no errors in the file.
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