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11.5 years ago
biorepine
★
1.5k
I am trying to run cuffmerge from the recently installed cufflinks 2.0.2 version. But it is giving me the following warning though I finally get the merged transcript. Any one faced this strange warning ?
/software/cufflinks-2.0.2.Linux_x86_64/cuffmerge -o thymus_cshl_cuffmerge -s /users/GR/mb/gbogu/software/mm9_illuminaIndexes/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -p 8 thcshlassemblies
[Fri Dec 28 21:12:00 2012] Beginning transcriptome assembly merge
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[Fri Dec 28 21:12:00 2012] Preparing output location thymus_cshl_cuffmerge/
Warning: no reference GTF provided!
[Fri Dec 28 21:12:05 2012] Converting GTF files to SAM
[21:12:05] Loading reference annotation.
[21:12:10] Loading reference annotation.
[Fri Dec 28 21:12:16 2012] Assembling transcripts
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o thymus_cshl_cuffmerge/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 thymus_cshl_cuffmerge/tmp/mergeSam_fileFLE8V7
[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 thymus_cshl_cuffmerge/tmp/mergeSam_fileFLE8V7 doesn't appear to be a valid BAM file, trying SAM...
[21:12:16] Inspecting reads and determining fragment length distribution.
Processed 42763 loci.
> Map Properties:
> Normalized Map Mass: 188971.00
> Raw Map Mass: 188971.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[21:12:22] Assembling transcripts and estimating abundances.
Processed 42763 loci.
[Fri Dec 28 21:21:59 2012] Comparing against reference file None
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
[Fri Dec 28 21:22:29 2012] Comparing against reference file None
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
