I suspect this could be due to errors in the GFF file, has any one seen it before? I am aligning 27 bp reads and I know that bowtie-build is in my path. I downloaded GTF file from UCSC and then converted it to GFF using the perl script on this forum. Any help will be REALLY appreciated.
/data/Mikkelson/SRX001940$ tophat -G /data/mouse2007_GFF_UCSC.txt /progs/tophat/mm9 SRR006806.fastq
[Fri Mar 5 12:27:37 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Fri Mar 5 12:27:37 2010] Preparing output location ./tophat_out/
[Fri Mar 5 12:27:37 2010] Checking for Bowtie index files
[Fri Mar 5 12:27:37 2010] Checking for reference FASTA file
[Fri Mar 5 12:27:37 2010] Checking for Bowtie
Bowtie version: 0.12.2.0
[Fri Mar 5 12:27:37 2010] Checking reads
seed length: 27bp
format: fastq
quality scale: phred33 (default)
[Fri Mar 5 12:29:37 2010] Reading known junctions from GFF file
[Fri Mar 5 12:31:25 2010] Mapping reads against mm9 with Bowtie
[Fri Mar 5 13:49:42 2010] Joining segment hits
[Fri Mar 5 13:52:08 2010] Searching for junctions via segment mapping
[Fri Mar 5 13:53:39 2010] Retrieving sequences for splices
[Fri Mar 5 13:53:40 2010] Indexing splices
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
Command: bowtie-build ./tophat_out/tmp/segment_juncs.fa ./tophat_out/tmp/segment_juncs
[FAILED]
Error: Splice sequence indexing failed with err = 1
Traceback (most recent call last):
File "/usr/bin/tophat", line 1635, in ?
sys.exit(main())
File "/usr/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/usr/bin/tophat", line 1456, in spliced_alignment
ref_fasta)
File "/usr/bin/tophat", line 981, in build_juncs_index
external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
File "/usr/bin/tophat", line 939, in build_juncs_bwt_index
exit(1)
TypeError: 'str' object is not callable
/data/Mikkelson/SRX001940$ tophat -G /data/mouse2007_GFF_UCSC.txt /progs/tophat/mm9 SRR006806.fastq
[Fri Mar 5 12:27:37 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Fri Mar 5 12:27:37 2010] Preparing output location ./tophat_out/
[Fri Mar 5 12:27:37 2010] Checking for Bowtie index files
[Fri Mar 5 12:27:37 2010] Checking for reference FASTA file
[Fri Mar 5 12:27:37 2010] Checking for Bowtie
Bowtie version: 0.12.2.0
[Fri Mar 5 12:27:37 2010] Checking reads
seed length: 27bp
format: fastq
quality scale: phred33 (default)
[Fri Mar 5 12:29:37 2010] Reading known junctions from GFF file
[Fri Mar 5 12:31:25 2010] Mapping reads against mm9 with Bowtie
[Fri Mar 5 13:49:42 2010] Joining segment hits
[Fri Mar 5 13:52:08 2010] Searching for junctions via segment mapping
[Fri Mar 5 13:53:39 2010] Retrieving sequences for splices
[Fri Mar 5 13:53:40 2010] Indexing splices
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
Command: bowtie-build ./tophat_out/tmp/segment_juncs.fa ./tophat_out/tmp/segment_juncs
[FAILED]
Error: Splice sequence indexing failed with err = 1
Traceback (most recent call last):
File "/usr/bin/tophat", line 1635, in ?
sys.exit(main())
File "/usr/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/usr/bin/tophat", line 1456, in spliced_alignment
ref_fasta)
File "/usr/bin/tophat", line 981, in build_juncs_index
external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
File "/usr/bin/tophat", line 939, in build_juncs_bwt_index
exit(1)
TypeError: 'str' object is not callable
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