I am getting this error:
Error in tophat:
[2013-02-13 20:46:41] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-13 20:46:41] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-13 20:46:41] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-13 20:46:41] Checking for Bowtie index files
[2013-02-13 20:46:41] Checking for reference FASTA file
Warning: Could not find FASTA file
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa
[2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/bin/bowtie2-inspect
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome >
./tophat_out/tmp/genome.fa
[2013-02-13 20:48:51] Generating SAM header for
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2013-02-13 20:49:23] Preparing reads
left reads: min. length=34, max. length=34, 2 kept reads (0 discarded)
Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about
half the read length because TopHat will work better with multiple
segments
[2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2
[2013-02-13 20:49:56] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option
(--no-coverage-search) if this step takes too much time or memory.
Warning: junction database is empty!
[2013-02-13 20:51:18] Reporting output tracks
[FAILED]
Error running /usr/local/bin/tophat_reports --min-anchor 8
--splice-mismatches 0 --min-report-intron 50 --max-report-intron
500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/
--max-multihits 20 --max-seg-multihits 40 --segment-length 25
--segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50
--max-closure-intron 5000 --min-coverage-intron 50
--max-coverage-intron 20000 --min-segment-intron 50
--max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2
--read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3
--max-deletion-length 3 -z gzip -p4 --no-closure-search
--no-microexon-search --sam-header
./tophat_out/tmp/genome_genome.bwt.samheader.sam
--report-discordant-pair-alignments --report-mixed-alignments
--samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty
2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5
--bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5
--bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa
./tophat_out/junctions.bed ./tophat_out/insertions.bed
./tophat_out/deletions.bed ./tophat_out/fusions.out
./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam
Loading ...done
What's wrong?