Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Timothy Amos
    replied
    This error can mean "correct version of bowtie not found"

    Originally posted by zorph View Post
    [Wed May 26 20:18:38 2010] Checking for Bowtie
    [FAILED]
    Error: bowtie not found on this system
    I recently got the same error:

    [2014-09-17 11:33:06] Checking for Bowtie
    Bowtie 2 not found, checking for older version..
    Error: Bowtie not found on this system.

    However, my issue was that the HPC admin had updated (the default version of) bowtie to a version that wasn't compatible with the installed version of tophat.
    I fixed this my removing that module and loading the old one (i.e. changing which version of bowtie was referred to on my path).

    http://ccb.jhu.edu/software/tophat/index.shtml lists which version of bowtie is compatible with which version of tophat.

    Leave a comment:


  • raela
    replied
    I would try another script to convert your files. I haven't done anything with solid myself, so I don't have any advice there, but the reads you posted didn't convert very well. There should be a logs/ directory in the tophat output directory with more information as to why it failed, but I'm suspicious of all of the Ns/low quality calls.

    Leave a comment:


  • zorph
    replied
    Originally posted by raela View Post
    You could also alter your PATH to include the bowtie directory. It depends on the shell you use (in linux, use `env | grep SHELL` to determine which this is). For example, bash is the default shell on my system, so in ~/.bashrc I have "export PATH=$PATH:/usr/local/genome/bin". You could add a similar line and point it to bowtie's location.

    Thank you so much for this piece of advice. Using it, I was able to get the test-reads to run; however, I was unable to get MY reads to run (see error message below).

    I gather there is something wrong with my reads. The sample is from solid and i used a script to convert them to a fastq format. The head of my fastq file is below the error message.

    Any help would be much appreciated. Thank YOU!

    ERROR MESSAGE
    [Thu Jun 3 12:57:27 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Thu Jun 3 12:57:27 2010] Preparing output location ./tophat_out/
    [Thu Jun 3 12:57:27 2010] Checking for Bowtie index files
    [Thu Jun 3 12:57:27 2010] Checking for reference FASTA file
    [Thu Jun 3 12:57:27 2010] Checking for Bowtie
    Bowtie version: 0.12.5.0
    [Thu Jun 3 12:57:27 2010] Checking reads
    seed length: 49bp
    format: fastq
    quality scale: phred33 (default)
    [FAILED]
    Error: could not execute prep_reads
    Traceback (most recent call last):
    File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 1635, in ?
    sys.exit(main())
    File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 1575, in main
    "left_kept_reads")
    File "/nethome/apps/ccsngs/apps/tophat/1.0.13/bin/tophat", line 799, in prep_reads
    exit(1)
    TypeError: 'str' object is not callable
    FASTQ FILE
    cat out.martin_ct8_d3.single.fq | head
    @/mihg/users/chumphries2/out.martin_ct8_d3:1_11_30/1
    CTNCGNNGNGNNNTGNNNAGNNNATCNTNGNGNCNNGNNGNGTCGNANC
    +
    -"%1-"(%-"-")-"%-"-"-"1%-"-"-"/%-"-"-"+%*-")-"&-")-"&-"-",-"-"%-"&'%%-")-"&
    @/mihg/users/chumphries2/out.martin_ct8_d3:1_12_50/1
    TGGGCNGGTGNGGGGNNNCCNNTCCCCGGGNCNGGNGGGGNGCGCNCNC
    +

    Leave a comment:


  • raela
    replied
    You could also alter your PATH to include the bowtie directory. It depends on the shell you use (in linux, use `env | grep SHELL` to determine which this is). For example, bash is the default shell on my system, so in ~/.bashrc I have "export PATH=$PATH:/usr/local/genome/bin". You could add a similar line and point it to bowtie's location.

    Leave a comment:


  • john_mu
    replied
    Hi zorph,

    You need to put bowtie in your path directory or the same directory as tophat.

    eg. if TopHat is in ~/programs/

    You also need to put Bowtie in ~/programs/

    ---

    Alternatively, you can put both in your "bin" folder such as

    /usr/bin

    If you do this, then you can run TopHat or Bowtie without specifying the path to the executable.

    EDIT: when I say put, I mean only move the executables there, not anything else and don't create any additional folders.

    Leave a comment:


  • zorph
    started a topic Proper installation of TopHat with Bowtie

    Proper installation of TopHat with Bowtie

    so I work in an institution where the CCS dept is responsible for installation.

    When trying to run TopHat, I get this output:

    [Wed May 26 20:18:38 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Wed May 26 20:18:38 2010] Preparing output location ./tophat_out/
    [Wed May 26 20:18:38 2010] Checking for Bowtie index files
    [Wed May 26 20:18:38 2010] Checking for reference FASTA file
    [Wed May 26 20:18:38 2010] Checking for Bowtie
    [FAILED]
    Error: bowtie not found on this system


    the way they installed tophat and bowtie is the following:
    ../a/b.directory_c/tophat/1.0.13/bin/tophat (stuff)
    ../a/b/directory_c/bowtie/0.12.5/bowtie (stuff)

    while I wouldn't mind moving stuff around to figure out how to get things to work, having them do it is painful (and time consuming). Can someone tell me how they ought to be orientated to run top hat properly

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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:47 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
54 views
0 likes
Last Post seqadmin  
Working...
X