Tophat Prep_Reads Error

Question

[Mohammad Reza Bakhtiarizadeh]

Hi I am running tophat on a test reads (Test data in tophat site and the code was tophat -r 20 test_ref reads_1.fq reads_2.fq) and got the following error (on linux, ubuntu)

[Thu Jul  5 03:45:02 2012] Beginning TopHat run (v1.3.3)
-----------------------------------------------
[Thu Jul  5 03:45:02 2012] Preparing output location ./tophat_out/
[Thu Jul  5 03:45:02 2012] Checking for Bowtie index files
[Thu Jul  5 03:45:02 2012] Checking for reference FASTA file
[Thu Jul  5 03:45:02 2012] Checking for Bowtie
    Bowtie version:             0.12.8.0
[Thu Jul  5 03:45:02 2012] Checking for Samtools
    Samtools Version: 0.1.18
[Thu Jul  5 03:45:02 2012] Generating SAM header for test_ref
[Thu Jul  5 03:45:02 2012] Preparing reads
    format:         fastq
    quality scale:     phred33 (default)
    [FAILED]
Error running 'prep_reads'

The prep_reads.log file has this information, /usr/bin/prep_reads: /lib/libz.so.1: version `ZLIB_1.2.3.3' not found (required by /usr/bin/prep_reads)

but i have libz.so.1 in lib (locate libz.so.1 is ok)

I really don't know what is the problem. if possible help me. thanks a lot in advance best

[samsara]

It seems tophat requires zib to run prep_reads. Install zlib version 1.2.3.3, it might work.

[Mohammad Reza Bakhtiarizadeh]

thanks i already installed zlib. i am a freshman about ubuntu, if possible tell me how can i be sure if zlib is installed or not. thanks again

[pinkiii1984v]

from your command line type: file /usr/lib64/libz.so.1 if you have libz installed then it will give you the /usr/lib64/libz.so.1 or a symbolic link to libz. If its not installed then i think you will get an error

Answer 1

[koukougogo]

If you are not the administrator, you need to make sure the libz.so is accessible for all user groups. Also add the path to the systems path variable.