another tophat "could not execute prep_reads" error

[James]

Hi,

Im getting this error:

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

[SongLi]

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.

Hi,

Im getting this error:

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

[James]

I fixed this problem. It may have been two things:

It may have been calling an older prep_reads I had lurking in my path.

It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

I'm running Mac OSX 10.5.8. by the way.

[SongLi]

Thank you James,

However, it may not be the reason, because in the log file you posted, it says v1.1.3 there.

I still have the problem on my side.

I fixed this problem. It may have been two things:

It may have been calling an older prep_reads I had lurking in my path.

It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

I'm running Mac OSX 10.5.8. by the way.

[SongLi]

Hi James,

Since you have solved the problem, would you mind post what the messages you get when the read RTF file passed?

On my side the error is:

[Tue Nov 16 17:02:17 2010] Reading known junctions from GTF file
[FAILED]
Error: could not execute prep_reads

That may help me to figure out what's wrong in my case.
Thanks,

I fixed this problem. It may have been two things:

It may have been calling an older prep_reads I had lurking in my path.

It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

I'm running Mac OSX 10.5.8. by the way.

[oliviera]

I have the same problem with tophat 1.1.3, and do not manage to solve the problem.

I used :
./tophat --solexa1.3-quals --no-novel-juncs -G Danio_rerio.Zv9.60.gtf -o /5cq15 Danio_rerio.Zv9.60 5.fastq

the log file is the same as yours:
prep_reads v1.1.3 (1680)
---------------------------
/home/olivier/src/illumina_software_version/tophat_113/bin/prep_reads: unrecognized option '--gtf-annotations'

Funny thing however in the gtf_juncs log file: seems to do something their
gtf_juncs v1.1.3 (1680)
---------------------------
Extracted 218405 junctions from /Danio_rerio.Zv9.60.gtf

I tried gtf and gff format and both failed.
When I run without -G option it works fine...
Any feedback would be much appreciated

Cheers

Oliviera

[oliviera]

I just tested the new release 1.1.4 and now the problem seems to be fixed!
Thanx a lot


Oliviera

[SongLi]

Thank you TopHat team for the timingly fix!

Don't know where to post, so I just post here.

I just tested the new release 1.1.4 and now the problem seems to be fixed!
Thanx a lot


Oliviera