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  • Cuffmerge error file never signals "done"...is this normal?

    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:

    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
    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:

    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]).
    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

  • #2
    Should be ok. I don't think cuffmerge writes a "done" message to the log file.

    Comment


    • #3
      Good to know, thanks so much!
      -Anna

      Comment

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