Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    a tophat running problem

    I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

    ../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

    [Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
    [Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie
    Bowtie version: 0.12.4.0
    [Fri Apr 9 13:17:33 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
    [Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
    [Fri Apr 9 13:17:34 2010] Indexing splices
    Traceback (most recent call last):
    File "../bin/tophat", line 1635, in ?
    sys.exit(main())
    File "../bin/tophat", line 1595, in main
    user_supplied_juncs)
    File "../bin/tophat", line 1456, in spliced_alignment
    ref_fasta)
    File "../bin/tophat", line 981, in build_juncs_index
    external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
    File "../bin/tophat", line 943, in build_juncs_bwt_index
    exit(1)
    TypeError: 'str' object is not callable
    Tags: None
  • #2
    Please help me out. I am sure many people here has experience with tophat. Could you please point me to the right direction how I could fix it?


    Originally posted by clariet View Post
    I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am wondering if anyone know what kind of problem it could be. Thanks!!!

    ../bin/tophat -r 20 test_ref reads_1.fq reads_2.fq

    [Fri Apr 9 13:17:33 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Apr 9 13:17:33 2010] Preparing output location ./tophat_out/
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie index files
    [Fri Apr 9 13:17:33 2010] Checking for reference FASTA file
    [Fri Apr 9 13:17:33 2010] Checking for Bowtie
    Bowtie version: 0.12.4.0
    [Fri Apr 9 13:17:33 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Fri Apr 9 13:17:33 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Joining segment hits
    Splitting reads into 3 segments
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Mapping reads against test_ref with Bowtie
    [Fri Apr 9 13:17:34 2010] Searching for junctions via segment mapping
    [Fri Apr 9 13:17:34 2010] Retrieving sequences for splices
    [Fri Apr 9 13:17:34 2010] Indexing splices
    Traceback (most recent call last):
    File "../bin/tophat", line 1635, in ?
    sys.exit(main())
    File "../bin/tophat", line 1595, in main
    user_supplied_juncs)
    File "../bin/tophat", line 1456, in spliced_alignment
    ref_fasta)
    File "../bin/tophat", line 981, in build_juncs_index
    external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
    File "../bin/tophat", line 943, in build_juncs_bwt_index
    exit(1)
    TypeError: 'str' object is not callable

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM
    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Expanding the Horizons of Cellular Research with the Single Cell Atlas by seqadmin
    Started by seqadmin, Today, 11:49 AM
    0 responses
    10 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    Today, 11:49 AM  
    Genetic Variants and Diabetes Risk in Childhood Cancer Survivors by seqadmin
    Started by seqadmin, Yesterday, 08:47 AM
    0 responses
    16 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    Yesterday, 08:47 AM  
    Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    61 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    04-11-2024, 12:08 PM  
    Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    60 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    04-10-2024, 10:19 PM  
    View All
    Working...
    X