some problem with tophat

[zslee]

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~~

[RockChalkJayhawk]

removed...I was in the wrong forum

[Cole Trapnell]

Originally Posted by zslee

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

[zslee]

yes, that works, thanks a lot !

[oxydeepu]

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

[NicoBxl]

maybe try the last version of tophat 1.4.1

Originally Posted by oxydeepu

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

[dpryan]

Originally Posted by oxydeepu

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).