Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • altodor
    replied
    Problem solved

    Hello, thank you!
    It really worked with 8 threads. First problem was, that I ran 16 treads of tophat on 8 cores and they tried to read to the same folder.
    Second problem, as appeared later, was the empty reference file. They say at tophat manual, that reference.fa will be built automatically with the first run of tophat. Nut I built in manually using bowtie-inspect. Now tophat produces junction database!

    Leave a comment:


  • Jon_Keats
    replied
    I've been using this version with 8 threads for a week now with no problems. did you build from source or download a binary? When in doubt build from source

    Leave a comment:


  • altodor
    started a topic tophat 1.2 multi thread mode error

    tophat 1.2 multi thread mode error

    Hi all,
    running tophat 1.2 with 8 threads the following errors occur

    srun: error: q44: tasks 0-6: Exited with exit code 1
    And one thread continues running.

    Also it seems like there is a conflict between threads in creating outputdirectory:
    :
    [Wed Jan 26 21:17:51 2011] Preparing output location tophat_04/
    Traceback (most recent call last):
    File "/soft/tophat-1.2.0/tophat", line 2347, in ?
    sys.exit(main())

    OSError: [Errno 17] File exists: '/tophat_04/'
    os.mkdir(output_dir)
    File "/soft/tophat-1.2.0/tophat", line 2230, in main
    sys.exit(main())

    Have anyone got the same problems?
    Last edited by altodor; 01-27-2011, 01:23 AM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X