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Old 01-01-2015, 05:28 AM   #1
Location: North Carolina

Join Date: Sep 2011
Posts: 38
Default tophat error with -G option

Hello all,

I'm trying to use tophat to run alignment.

Tophat version: tophat/2.0.12
Bowtie version: bowtie2/2.2.1

here is my command line for the job:
tophat -G amel_OGSv3.2.gff3 --no-novel-juncs /gpfs_share/xxxx/xxxx/trim/xxxx.fastq

Below is the error I got:

[2015-01-01 09:22:31] Beginning TopHat run (v2.0.12)
[2015-01-01 09:22:31] Checking for Bowtie
Bowtie version:
[2015-01-01 09:22:31] Checking for Samtools
Samtools version:
[2015-01-01 09:22:31] Checking for Bowtie index files (genome)..
[2015-01-01 09:22:31] Checking for reference FASTA file
[2015-01-01 09:22:31] Generating SAM header for Am_genome
Traceback (most recent call last):
File "/usr/local/apps/tophat/2.0.12-gcc454/bin/tophat", line 4087, in <module>
File "/usr/local/apps/tophat/2.0.12-gcc454/bin/tophat", line 3941, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/local/apps/tophat/2.0.12-gcc454/bin/tophat", line 1836, in check_reads_format
zf = ZReader(f_name, params)
File "/usr/local/apps/tophat/2.0.12-gcc454/bin/tophat", line 1789, in __init__
IOError: [Errno 2] No such file or directory: '-G'
I have checked the first column of my gff3 and bowtie2 index, and they match.

I'm running this on a cluster.

thank you so much.

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