I have spent the whole day now trying to get past this error: I have tried everything. UCSC GTF file, NCBI GTF file (converted it to GFF) but I keep getting this error. Can someone please help me? I have made sure the chr names are the same as in my index.
[Fri Apr 23 17:10:16 2010] Retrieving sequences for splices
[Fri Apr 23 17:10:16 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
example GFF I used:
chr1 mm9_knownGene gene 4481009 4486494 0.000000 - . ID=uc007afc.1;Name=
chr1 mm9_knownGene mRNA 4481009 4486494 0.000000 - . ID=uc007afc.1;Name=;Parent=uc007afc.1
chr1 mm9_knownGene exon 4481009 4482749 0.000000 - . ID=uc007afc.1.;Name=;Parent=uc007afc.1
ch
[Fri Apr 23 17:10:16 2010] Retrieving sequences for splices
[Fri Apr 23 17:10:16 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
example GFF I used:
chr1 mm9_knownGene gene 4481009 4486494 0.000000 - . ID=uc007afc.1;Name=
chr1 mm9_knownGene mRNA 4481009 4486494 0.000000 - . ID=uc007afc.1;Name=;Parent=uc007afc.1
chr1 mm9_knownGene exon 4481009 4482749 0.000000 - . ID=uc007afc.1.;Name=;Parent=uc007afc.1
ch
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