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Old 11-16-2010, 10:19 AM   #2
SongLi
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Location: Durham

Join Date: Oct 2010
Posts: 19
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I got the same error for my dataset today, without those options:

tophat -o Mytophat_out -G mygtf.gtf indexes/myindex reads/myreads.fasta

The error message is :

[FAILED]
Error: could not execute prep_reads


and in the prep_reads.log is:

prep_reads v1.1.3 (1680)
---------------------------
somedir/prep_reads: unrecognized option `--gtf-annotations'


Hope someone can help.


Quote:
Originally Posted by James View Post
Hi,

Im getting this error:
Code:
tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq


[Mon Nov 15 12:52:59 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Mon Nov 15 12:52:59 2010] Preparing output location RNA-seq-14.11.10/tophat_out_0H//
[Mon Nov 15 12:52:59 2010] Checking for Bowtie index files
[Mon Nov 15 12:52:59 2010] Checking for reference FASTA file
[Mon Nov 15 12:52:59 2010] Checking for Bowtie
	Bowtie version:			 0.12.7.0
[Mon Nov 15 12:52:59 2010] Checking for Samtools
	Samtools version:		 0.1.9.0
[Mon Nov 15 12:52:59 2010] Checking reads
	min read length: 36bp, max read length: 36bp
	format:		 fastq
	quality scale:	 phred64 (reads generated with GA pipeline version >= 1.3)
[Mon Nov 15 12:55:49 2010] Reading known junctions from GTF file
	[FAILED]
Error: could not execute prep_reads
I check the log file for prep_reads it has:

prep_reads v1.1.3 (1680)
---------------------------
prep_reads: unrecognized option `--gtf-annotations'

Anybody had this error? or can help? Thanks James

Last edited by SongLi; 11-16-2010 at 10:21 AM.
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