TopHat prep_reads error

[mikeyt]

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!

[Jane Lee]

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!