Tweet
Hello all,
I'm fairly new to the bioinformatics world and am trying to combine several gtf files with cuffmerge. My shell script is as follows:
where gtf names is a text file containing the gtf filenames, one per line. The job seems to run to completion, producing the expected merged.gtf. However, an error fie is also produced stating the following:
My concern is that the error file never gives a "done" message to indicate successful completion...is this to be expected? Thank you in advance for your help!
-Anna
I'm fairly new to the bioinformatics world and am trying to combine several gtf files with cuffmerge. My shell script is as follows:
Code:
#!/bin/bash /home/usr/bin/cufflinks-2.2.1.Linux_x86_64/cuffmerge -p 8 -s /home/usr/hg19_genome/hg19.mfa gtf_names
Code:
[Thu Jul 9 15:29:39 2015] Beginning transcriptome assembly merge ------------------------------------------- [Thu Jul 9 15:29:39 2015] Preparing output location ./merged_asm/ Warning: no reference GTF provided! [Thu Jul 9 15:29:39 2015] Converting GTF files to SAM [15:29:39] Loading reference annotation. [15:29:39] Loading reference annotation. [15:29:39] Loading reference annotation. [15:29:39] Loading reference annotation. [15:29:39] Loading reference annotation. [15:29:39] Loading reference annotation. [Thu Jul 9 15:29:39 2015] Assembling transcripts Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website ([url]http://cufflinks.cbcb.umd.edu[/url]). Command line: cufflinks -o ./merged_asm/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_fileEPMs7s [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_fileEPMs7s doesn't appear to be a valid BAM file, trying SAM... [15:29:39] Inspecting reads and determining fragment length distribution. Processed 124 loci. > Map Properties: > Normalized Map Mass: 951.00 > Raw Map Mass: 951.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [15:29:39] Assembling transcripts and estimating abundances. Processed 126 loci. [Thu Jul 9 15:29:40 2015] Comparing against reference file None Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website ([url]http://cufflinks.cbcb.umd.edu[/url]). [Thu Jul 9 15:29:42 2015] Comparing against reference file None Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website ([url]http://cufflinks.cbcb.umd.edu[/url]).
-Anna
Comment