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Old 10-31-2012, 04:17 PM   #1
mikeyt
Junior Member
 
Location: US

Join Date: Oct 2012
Posts: 3
Default TopHat prep_reads error

Hi all,

I am new to the UNIX system and RNA-seq analysis in general. I have just installed the binary of tophat and run into problems when trying to run the test install with the test data.

After running the command: tophat -r 20 test_ref reads_1.fq reads_2.fq , I get the following:

[2012-10-31 16:43:46] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2012-10-31 16:43:46] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-10-31 16:43:46] Checking for Samtools
Samtools version: 0.1.18.0
[2012-10-31 16:43:46] Checking for Bowtie index files
[2012-10-31 16:43:46] Checking for reference FASTA file
[2012-10-31 16:43:46] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2012-10-31 16:43:47] Preparing reads
[FAILED]
Error running 'prep_reads'
prep_reads [--filter-multi <multi.fq>] <reads1.fa/fq,...,readsN.fa/fq> [<read_qual_files>,..] \[<mate_reads1.fa/fq,...,mate_readsN.fa/fq> [<mate_qual_files>,..]


Any help or suggestions is much appreciated.

Thanks!
mikeyt is offline   Reply With Quote
Old 02-27-2013, 05:11 PM   #2
Jane Lee
Junior Member
 
Location: China

Join Date: Feb 2013
Posts: 6
Default

Quote:
Originally Posted by mikeyt View Post
Hi all,

I am new to the UNIX system and RNA-seq analysis in general. I have just installed the binary of tophat and run into problems when trying to run the test install with the test data.

After running the command: tophat -r 20 test_ref reads_1.fq reads_2.fq , I get the following:

[2012-10-31 16:43:46] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2012-10-31 16:43:46] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-10-31 16:43:46] Checking for Samtools
Samtools version: 0.1.18.0
[2012-10-31 16:43:46] Checking for Bowtie index files
[2012-10-31 16:43:46] Checking for reference FASTA file
[2012-10-31 16:43:46] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2012-10-31 16:43:47] Preparing reads
[FAILED]
Error running 'prep_reads'
prep_reads [--filter-multi <multi.fq>] <reads1.fa/fq,...,readsN.fa/fq> [<read_qual_files>,..] \[<mate_reads1.fa/fq,...,mate_readsN.fa/fq> [<mate_qual_files>,..]


Any help or suggestions is much appreciated.

Thanks!

Hi,

I met the same problem with tophat running, if you have solved the problem, could you share the solution with me?

Thank you very much!
Best wishes!
Jane Lee is offline   Reply With Quote
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