I'm tring to merge my transcript data produced from 8 samples analysed using TopHat and compiled using Cufflinks. Unfortunately when i run cuffmerge I get an error message about "missing fasta data files for 'Mt' and 'Pt'" but can't find reference to these files anywhere else in the literature or on-line?
Any advice greatfully received.
richard@ubuntu:~/RNA_seq_analysis/Cuffmerge$ cuffmerge -g arabidopsis_thaliana.TAIR10.60.gtf -s TAIR10_chr_all.fas -p 6 run297_transcript_cuffmerge.txt
[Thu Aug 9 15:36:29 2012] Beginning transcriptome assembly merge
-------------------------------------------
[Thu Aug 9 15:36:29 2012] Preparing output location ./merged_asm/
[Thu Aug 9 15:36:36 2012] Converting GTF files to SAM
[15:36:36] Loading reference annotation.
[15:36:37] Loading reference annotation.
[15:36:38] Loading reference annotation.
[15:36:39] Loading reference annotation.
[15:36:40] Loading reference annotation.
[15:36:41] Loading reference annotation.
[15:36:42] Loading reference annotation.
[15:36:44] Loading reference annotation.
[Thu Aug 9 15:36:45 2012] Quantitating transcripts
You are using Cufflinks v2.0.2, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g arabidopsis_thaliana.TAIR10.60.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 6 ./merged_asm/tmp/mergeSam_filejHHJWI
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_filejHHJWI doesn't appear to be a valid BAM file, trying SAM...
[15:36:45] Loading reference annotation.
[15:36:47] Inspecting reads and determining fragment length distribution.
Processed 26332 loci.
> Map Properties:
> Normalized Map Mass: 194074.00
> Raw Map Mass: 194074.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[15:36:48] Assembling transcripts and estimating abundances.
Processed 26332 loci.
[Thu Aug 9 15:44:22 2012] Comparing against reference file arabidopsis_thaliana.TAIR10.60.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
No fasta index found for TAIR10_chr_all.fas. Rebuilding, please wait..
Fasta index rebuilt.
Warning: couldn't find fasta record for 'Mt'!
Warning: couldn't find fasta record for 'Pt'!
[Thu Aug 9 15:44:34 2012] Comparing against reference file arabidopsis_thaliana.TAIR10.60.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
Warning: couldn't find fasta record for 'Mt'!
Warning: couldn't find fasta record for 'Pt'!
Any advice greatfully received.
richard@ubuntu:~/RNA_seq_analysis/Cuffmerge$ cuffmerge -g arabidopsis_thaliana.TAIR10.60.gtf -s TAIR10_chr_all.fas -p 6 run297_transcript_cuffmerge.txt
[Thu Aug 9 15:36:29 2012] Beginning transcriptome assembly merge
-------------------------------------------
[Thu Aug 9 15:36:29 2012] Preparing output location ./merged_asm/
[Thu Aug 9 15:36:36 2012] Converting GTF files to SAM
[15:36:36] Loading reference annotation.
[15:36:37] Loading reference annotation.
[15:36:38] Loading reference annotation.
[15:36:39] Loading reference annotation.
[15:36:40] Loading reference annotation.
[15:36:41] Loading reference annotation.
[15:36:42] Loading reference annotation.
[15:36:44] Loading reference annotation.
[Thu Aug 9 15:36:45 2012] Quantitating transcripts
You are using Cufflinks v2.0.2, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g arabidopsis_thaliana.TAIR10.60.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 6 ./merged_asm/tmp/mergeSam_filejHHJWI
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_filejHHJWI doesn't appear to be a valid BAM file, trying SAM...
[15:36:45] Loading reference annotation.
[15:36:47] Inspecting reads and determining fragment length distribution.
Processed 26332 loci.
> Map Properties:
> Normalized Map Mass: 194074.00
> Raw Map Mass: 194074.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[15:36:48] Assembling transcripts and estimating abundances.
Processed 26332 loci.
[Thu Aug 9 15:44:22 2012] Comparing against reference file arabidopsis_thaliana.TAIR10.60.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
No fasta index found for TAIR10_chr_all.fas. Rebuilding, please wait..
Fasta index rebuilt.
Warning: couldn't find fasta record for 'Mt'!
Warning: couldn't find fasta record for 'Pt'!
[Thu Aug 9 15:44:34 2012] Comparing against reference file arabidopsis_thaliana.TAIR10.60.gtf
You are using Cufflinks v2.0.2, which is the most recent release.
Warning: couldn't find fasta record for 'Mt'!
Warning: couldn't find fasta record for 'Pt'!
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