Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat2 running test_data Errno 8 failed to Index splices

    Hello,
    I am running into problems when trying to get Tophat2 set up following this tutorial: https://ccb.jhu.edu/software/tophat/tutorial.shtml
    I have Bowtie2, Bowtie2-build, and bowtie2-insect in my path as well as the directory to my tophat2 file.
    When I run the command [tophat2 -r 20 test_ref reads_1.fq reads_2.fq]
    I get the following message:
    [2019-06-04 09:43:21] Beginning TopHat run (v2.1.1)
    -----------------------------------------------
    [2019-06-04 09:43:21] Checking for Bowtie
    Bowtie 2 not found, checking for older version..
    Bowtie version: 1.1.2.0
    [2019-06-04 09:43:21] Checking for Bowtie index files (genome)..
    Found both Bowtie1 and Bowtie2 indexes.
    [2019-06-04 09:43:21] Checking for reference FASTA file
    [2019-06-04 09:43:21] Generating SAM header for test_ref
    [2019-06-04 09:43:21] Preparing reads
    left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    [2019-06-04 09:43:21] Mapping left_kept_reads to genome test_ref with Bowtie
    [2019-06-04 09:43:21] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    [2019-06-04 09:43:21] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    [2019-06-04 09:43:21] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    [2019-06-04 09:43:21] Mapping right_kept_reads to genome test_ref with Bowtie
    [2019-06-04 09:43:21] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
    [2019-06-04 09:43:22] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
    [2019-06-04 09:43:22] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
    [2019-06-04 09:43:22] Searching for junctions via segment mapping
    [2019-06-04 09:43:22] Retrieving sequences for splices
    [2019-06-04 09:43:22] Indexing splices
    [FAILED]
    [Errno 8] Exec format error

    I have seen that others have discovered they have installed the wrong type however I have check and I have installed bowtie2-2.3.3.1-linux-x86_64 and tophat-2.1.1.Linux_x86_64 on my windows system working on a 64 bit PuTTY system.
    Sorry for the drawn out question, I'm fairly new to this and wanted to provide as much info as I could.
    Thanks in advance for anyone who could help

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
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X