Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM
      • seqadmin
        The Impact of AI in Genomic Medicine
        by seqadmin



        Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
        02-26-2024, 02:07 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-14-2024, 06:13 AM
      0 responses
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      81 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-06-2024, 09:51 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X