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Old 12-15-2012, 03:43 AM   #1
vaibhavvsk
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Location: Pune

Join Date: Sep 2011
Posts: 14
Post Tophat Linux x86_64 binary Error

I have downloaded the Linux x86_64 binary. I'm trying to run tophat on the the data using command given as follows :

COMMAND:

$ tophat /opt/reference_indexes/bowtie2_index/bowtie2_prebuilt_ref_index/hg19/hg19 r 200 --keep -tmp /media/LUN1/RNA-Seq_DATA/Project_AC069EACXX/Sample_1221745/concated/1221745_CGATGT_L006_R1.fastq /media/LUN1/RNA-Seq_DATA/Project_AC069EACXX/Sample_1221745/concated/1221745_CGATGT_L006_R2.fastq

STDOUT:

[2012-12-15 15:51:38] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2012-12-15 15:51:38] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-12-15 15:51:38] Checking for Samtools
Samtools version: 0.1.18.0
[2012-12-15 15:51:38] Checking for Bowtie index files
[2012-12-15 15:51:38] Checking for reference FASTA file
Warning: Could not find FASTA file /opt/reference_indexes/bowtie2_index/bowtie2_prebuilt_ref_index/hg19/hg19.fa
[2012-12-15 15:51:38] Reconstituting reference FASTA file from Bowtie index
Executing: /opt/ngs_softwares/tophat-2.0.6/bowtie2-inspect /opt/reference_indexes/bowtie2_index/bowtie2_prebuilt_ref_index/hg19/hg19 > ./tophat_out/tmp/hg19.fa
[2012-12-15 15:54:17] Generating SAM header for /opt/reference_indexes/bowtie2_index/bowtie2_prebuilt_ref_index/hg19/hg19
Traceback (most recent call last):
File "/opt/ngs_softwares/tophat-2.0.6/tophat", line 4022, in <module>
sys.exit(main())
File "/opt/ngs_softwares/tophat-2.0.6/tophat", line 3877, in main
params.read_params = check_reads_format(params, reads_list)
File "/opt/ngs_softwares/tophat-2.0.6/tophat", line 1814, in check_reads_format
zf = ZReader(f_name, params)
File "/opt/ngs_softwares/tophat-2.0.6/tophat", line 1767, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: '\xe2\x80\x93r'


Whether anyone has came across the issue, please reply the solution to this issue.
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Vaibhav Kulkarni
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Old 12-17-2012, 02:57 AM   #2
RocheKermit
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Location: Luxembourg

Join Date: Nov 2011
Posts: 15
Default

Is there a space between --keep and -tmp?
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