Tophat Error: No unambiguous stretches of characters in the input(?).

[thinkRNA]

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

[lakshmaa]

Error: No unambiguous stretches of characters in the input. Aborting...

I have this same error. Can anyone please tell me why this is happening.


[Tue Sep 20 15:26:25 2011] Reading known junctions from GTF file
[Tue Sep 20 15:27:39 2011] Mapping reads against zv9 with Bowtie
[Tue Sep 20 16:47:01 2011] Joining segment hits
[Tue Sep 20 16:53:45 2011] Mapping reads against zv9 with Bowtie(1/4)
[Tue Sep 20 17:40:17 2011] Mapping reads against zv9 with Bowtie(2/4)
[Tue Sep 20 18:25:21 2011] Mapping reads against zv9 with Bowtie(3/4)
[Tue Sep 20 19:12:59 2011] Mapping reads against zv9 with Bowtie(4/4)
[Tue Sep 20 20:55:40 2011] Searching for junctions via segment mapping
[Tue Sep 20 20:57:48 2011] Retrieving sequences for splices
[Tue Sep 20 21:01:18 2011] Indexing splices
Warning: Empty input file
Error: No unambiguous stretches of characters in the input. Aborting...
Command: bowtie-build tophat_BC4_gtf_mix1/tmp/segment_juncs.fa tophat_BC4_gtf_mi
x1/tmp/segment_juncs
[FAILED]
Error: Splice sequence indexing failed with err = 1


Thanks

[suzifei]

Me three

Has anyone figured out what causes this error?

Thanks,
Suzi