Can anyone here help me with the tophat error?
when i map single-end solid sequences(fastq format) to hg18 as follow:
tophat --solexa1.3-quals /usr/local/bowtie/indexes/hg18 s_1_1.fastq
there is such error:
[Thu Jan 14 09:28:00 2010] Beginning TopHat run (v1.0.10)
-----------------------------------------------
[Thu Jan 14 09:28:00 2010] Preparing output location ./tophat_out/
[Thu Jan 14 09:28:00 2010] Checking for Bowtie index files
[Thu Jan 14 09:28:00 2010] Checking for reference FASTA file
[Thu Jan 14 09:28:00 2010] Checking for Bowtie
Bowtie version: 0.10.1.0
[Thu Jan 14 09:28:00 2010] Checking reads
seed length: 76bp
format: fastq
quality scale: --solexa1.3-quals
Splitting reads into 3 segments
[Thu Jan 14 09:52:04 2010] Mapping reads against hg18 with Bowtie
[FAILED]
Error: could not execute Bowtie
Traceback (most recent call last):
File "/usr/local/tophat-1.0.10/bin/tophat", line 1490, in ?
sys.exit(main())
File "/usr/local/tophat-1.0.10/bin/tophat", line 1462, in main
user_supplied_juncs)
File "/usr/local/tophat-1.0.10/bin/tophat", line 1241, in spliced_alignment
seg)
File "/usr/local/tophat-1.0.10/bin/tophat", line 752, in bowtie
exit(1)
TypeError: 'str' object is not callable
What could be wrong?
can anyone help me? thanks in advance~~
when i map single-end solid sequences(fastq format) to hg18 as follow:
tophat --solexa1.3-quals /usr/local/bowtie/indexes/hg18 s_1_1.fastq
there is such error:
[Thu Jan 14 09:28:00 2010] Beginning TopHat run (v1.0.10)
-----------------------------------------------
[Thu Jan 14 09:28:00 2010] Preparing output location ./tophat_out/
[Thu Jan 14 09:28:00 2010] Checking for Bowtie index files
[Thu Jan 14 09:28:00 2010] Checking for reference FASTA file
[Thu Jan 14 09:28:00 2010] Checking for Bowtie
Bowtie version: 0.10.1.0
[Thu Jan 14 09:28:00 2010] Checking reads
seed length: 76bp
format: fastq
quality scale: --solexa1.3-quals
Splitting reads into 3 segments
[Thu Jan 14 09:52:04 2010] Mapping reads against hg18 with Bowtie
[FAILED]
Error: could not execute Bowtie
Traceback (most recent call last):
File "/usr/local/tophat-1.0.10/bin/tophat", line 1490, in ?
sys.exit(main())
File "/usr/local/tophat-1.0.10/bin/tophat", line 1462, in main
user_supplied_juncs)
File "/usr/local/tophat-1.0.10/bin/tophat", line 1241, in spliced_alignment
seg)
File "/usr/local/tophat-1.0.10/bin/tophat", line 752, in bowtie
exit(1)
TypeError: 'str' object is not callable
What could be wrong?
can anyone help me? thanks in advance~~
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