Tophat error -Junction database is empty

[repinementer]

I built hg18 indexes in bowtie and I also placed those files in testdata folder
Could any one please help how to get rid off this???

Thanx

[Mon Aug  2 21:20:14 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Mon Aug  2 21:21:59 2010] Joining segment hits
[Mon Aug  2 21:21:59 2010] Joining segment hits
[Mon Aug  2 21:21:59 2010] Reporting output tracks
        [FAILED]
Error: Report generation failed with err = 1

[repinementer]

May be I should post the whole error

I tried with and with out segment length advanced option bylooking at your answers in previous thread. but no luck!

[B]
$ tophat -r 156 hg18_c SRR015270_1.fastq SRR015271_1.fastq [/B][B]SRR015272_1.fastq SRR015273_1.fastq [/B]

[Mon Aug  2 21:40:27 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Aug  2 21:40:27 2010] Preparing output location ./tophat_out/
[Mon Aug  2 21:40:27 2010] Checking for Bowtie index files
[Mon Aug  2 21:40:27 2010] Checking for reference FASTA file
[Mon Aug  2 21:40:27 2010] Checking for Bowtie
        Bowtie version:          0.12.5.0
[Mon Aug  2 21:40:27 2010] Checking reads
        seed length:     32bp
        format:          fastq
        quality scale:   phred33 (default)
[Mon Aug  2 21:41:29 2010] Mapping reads against hg18_c with Bowtie
[Mon Aug  2 21:41:29 2010] Joining segment hits
[Mon Aug  2 21:41:29 2010] Mapping reads against hg18_c with Bowtie
[Mon Aug  2 21:41:29 2010] Joining segment hits
[Mon Aug  2 21:41:29 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Mon Aug  2 21:43:13 2010] Joining segment hits
[Mon Aug  2 21:43:14 2010] Joining segment hits
[Mon Aug  2 21:43:14 2010] Reporting output tracks
        [FAILED]
Error: Report generation failed with err = 1
Traceback (most recent call last):
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1635, in ?
    sys.exit(main())
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1607, in main
    params.gff_annotation)
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1044, in compile_reports
    exit(1)
TypeError: 'str' object is not callable

$tophat -r 156 --segment-length 32 hg18_c SRR015270_1.fastq SRR015271_1.fastq SRR015272_1.fastq SRR015273_1.fastq 

[Mon Aug  2 22:04:45 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Aug  2 22:04:45 2010] Preparing output location ./tophat_out/
[Mon Aug  2 22:04:45 2010] Checking for Bowtie index files
[Mon Aug  2 22:04:45 2010] Checking for reference FASTA file
[Mon Aug  2 22:04:45 2010] Checking for Bowtie
        Bowtie version:          0.12.5.0
[Mon Aug  2 22:04:45 2010] Checking reads
        seed length:     32bp
        format:          fastq
        quality scale:   phred33 (default)
[Mon Aug  2 22:05:47 2010] Mapping reads against hg18_c with Bowtie
[Mon Aug  2 22:05:47 2010] Joining segment hits
[Mon Aug  2 22:05:47 2010] Mapping reads against hg18_c with Bowtie
[Mon Aug  2 22:05:47 2010] Joining segment hits
[Mon Aug  2 22:05:47 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Mon Aug  2 22:07:32 2010] Joining segment hits
[Mon Aug  2 22:07:32 2010] Joining segment hits
[Mon Aug  2 22:07:32 2010] Reporting output tracks
        [FAILED]
Error: Report generation failed with err = 1
Traceback (most recent call last):
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1635, in ?
    sys.exit(main())
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1607, in main
    params.gff_annotation)
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1044, in compile_reports
    exit(1)
TypeError: 'str' object is not callable

segment_junctionLogs

[bogugk@Trivia logs]$ cat segment_juncs.log 
segment_juncs v1.0.13
---------------------------
Loading reference sequences...
        Loading chr1...done
        Loading chr2...done
        Loading chr3...done
        Loading chr4...done
        Loading chr5...done
        Loading chr6...done
        Loading chr7...done
        Loading chr8...done
        Loading chr9...done
        Loading chr10...done
        Loading chr11...done
        Loading chr12...done
        Loading chr13...done
        Loading chr14...done
        Loading chr15...done
        Loading chr16...done
        Loading chr17...done
        Loading chr18...done
        Loading chr19...done
        Loading chr20...done
        Loading chr21...done
        Loading chr22...done
        Loading chrX...done
        Loading chrY...done
        Loading chrM...done
Found 0 potential split-segment junctions
Indexing extensions in ./tophat_out/tmp//left_kept_reads_missing.fq
Can't open file ./tophat_out/tmp//left_kept_reads_missing.fq for reading, skipping...
Indexing extensions in ./tophat_out/tmp//right_kept_reads_missing.fq
Can't open file ./tophat_out/tmp//right_kept_reads_missing.fq for reading, skipping...
Looking for junctions by island end pairings
Adding hits from segment file 0 to coverage map
Adding hits from segment file 1 to coverage map
Map covers 0 bases
Map covers 0 bases in sufficiently long segments
Map contains 1 good islands
0 are left looking bases
0 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Found 0 potential island-end pairing junctions
done
Reporting potential splice junctions...done
Reported 0 total possible splices