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Old 10-27-2009, 03:38 AM   #1
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default some problem with tophat

has anyone here used tophat ?
when i map single-end solid sequences(fastq format) to hg18 as follow:
~/bin/tophat bowtie-0.11.3_index/hg18 query.fq -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4

there is such error:
Error: you must set the mean inner distance between mates with -r
Traceback (most recent call last):
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1487, in ?
sys.exit(main())
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1402, in main
exit(1)
TypeError: 'str' object is not callable

what's going on ?
can anyone help me? thanks in advance~~
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Old 10-30-2009, 05:48 AM   #2
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191
Wink Wrong forum

removed...I was in the wrong forum

Last edited by RockChalkJayhawk; 10-30-2009 at 10:10 AM.
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Old 10-30-2009, 09:17 AM   #3
Cole Trapnell
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Location: Boston, MA

Join Date: Nov 2008
Posts: 212
Default

Quote:
Originally Posted by zslee View Post
has anyone here used tophat ?
when i map single-end solid sequences(fastq format) to hg18 as follow:
~/bin/tophat bowtie-0.11.3_index/hg18 query.fq -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4

there is such error:
Error: you must set the mean inner distance between mates with -r
Traceback (most recent call last):
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1487, in ?
sys.exit(main())
File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1402, in main
exit(1)
TypeError: 'str' object is not callable

what's going on ?
can anyone help me? thanks in advance~~
In the command above, you are placing the arguments (the index name and the FASTQ file of your reads) before the options. It should be:

tophat -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4 bowtie-0.11.3_index/hg18 query.fq
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Old 10-30-2009, 03:53 PM   #4
zslee
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Location: shanghai of china

Join Date: May 2009
Posts: 29
Default

yes, that works, thanks a lot !
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Old 04-03-2012, 10:35 PM   #5
oxydeepu
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Location: bangalore,india

Join Date: Jul 2011
Posts: 41
Default Similiar sort of problem.

Hi all,

I am getting this error

Traceback (most recent call last):
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2607, in ?
sys.exit(main())
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2504, in main
params.read_params = check_reads_format(params, reads_list)
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1234, in check_reads_format
zf = ZReader(f_name, params.system_params)
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1185, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: '-o'


while running tophat

tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &

Please help me with this error.

Thanking you in advance.

Regards
Deepak
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Old 04-04-2012, 02:03 AM   #6
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 263
Default

maybe try the last version of tophat 1.4.1

Quote:
Originally Posted by oxydeepu View Post
Hi all,

I am getting this error

Traceback (most recent call last):
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2607, in ?
sys.exit(main())
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2504, in main
params.read_params = check_reads_format(params, reads_list)
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1234, in check_reads_format
zf = ZReader(f_name, params.system_params)
File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1185, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: '-o'


while running tophat

tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &

Please help me with this error.

Thanking you in advance.

Regards
Deepak
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Old 04-04-2012, 02:24 AM   #7
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Quote:
Originally Posted by oxydeepu View Post
tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &
Aside from using a newer version, you might try "tophat -o tophat_new -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq" instead. Depending on how tophat parses how it's called, what you wrote as a command could cause an issue (the error suggests that it's trying to open a file called "-o", suggesting that it's not seeing that as an option but a file name).
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