Hi all, I have a cuffmerge problem. It says "EOF marker is absent. The input is probably truncated". I have run tophat and cufflinks successfully. What does this mean??
Thanks.
G
[gonzalo@localhost trimmed_reads]$ cuffmerge -g genes.gtf -s genome.fa -p 20 assemblies.txt
[Sat Sep 13 12:33:25 2014] Beginning transcriptome assembly merge
-------------------------------------------
[Sat Sep 13 12:33:25 2014] Preparing output location ./merged_asm/
[Sat Sep 13 12:33:35 2014] Converting GTF files to SAM
[12:33:35] Loading reference annotation.
[12:33:37] Loading reference annotation.
[12:33:40] Loading reference annotation.
[12:33:43] Loading reference annotation.
[12:33:45] Loading reference annotation.
[12:33:48] Loading reference annotation.
[Sat Sep 13 12:33:51 2014] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g genes.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 20 ./merged_asm/tmp/mergeSam_fileJRPl29
[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 ./merged_asm/tmp/mergeSam_fileJRPl29 doesn't appear to be a valid BAM file, trying SAM...
[12:33:51] Loading reference annotation.
[12:33:57] Inspecting reads and determining fragment length distribution.
Processed 28060 loci.
Map Properties:
Normalized Map Mass: 154834.00
Raw Map Mass: 154834.00
Fragment Length Distribution: Truncated Gaussian (default)
Default Mean: 200
Default Std Dev: 80
[12:33:59] Assembling transcripts and estimating abundances.
Processed 28060 loci.
[Sat Sep 13 12:34:11 2014] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
[Sat Sep 13 12:34:34 2014] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
Thanks.
G
[gonzalo@localhost trimmed_reads]$ cuffmerge -g genes.gtf -s genome.fa -p 20 assemblies.txt
[Sat Sep 13 12:33:25 2014] Beginning transcriptome assembly merge
-------------------------------------------
[Sat Sep 13 12:33:25 2014] Preparing output location ./merged_asm/
[Sat Sep 13 12:33:35 2014] Converting GTF files to SAM
[12:33:35] Loading reference annotation.
[12:33:37] Loading reference annotation.
[12:33:40] Loading reference annotation.
[12:33:43] Loading reference annotation.
[12:33:45] Loading reference annotation.
[12:33:48] Loading reference annotation.
[Sat Sep 13 12:33:51 2014] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g genes.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 20 ./merged_asm/tmp/mergeSam_fileJRPl29
[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 ./merged_asm/tmp/mergeSam_fileJRPl29 doesn't appear to be a valid BAM file, trying SAM...
[12:33:51] Loading reference annotation.
[12:33:57] Inspecting reads and determining fragment length distribution.
Processed 28060 loci.
Map Properties:
Normalized Map Mass: 154834.00
Raw Map Mass: 154834.00
Fragment Length Distribution: Truncated Gaussian (default)
Default Mean: 200
Default Std Dev: 80
[12:33:59] Assembling transcripts and estimating abundances.
Processed 28060 loci.
[Sat Sep 13 12:34:11 2014] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
[Sat Sep 13 12:34:34 2014] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
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