Tophat 2.0.9 only output chr1-7 in junctions.bed

[fabrice]

The log file segment_juncs.log

segment_juncs v2.0.9 (4112M)
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[samopen] SAM header is present: 84 sequences.
Loading reference sequences...
Loading chr1...done
Loading chr2...done
Loading chr3...done
Loading chr4...done
Loading chr5...done
Loading chr6...done
Loading chr7...done
>> Performing segment-search:
found 0 potential split-segment junctions
found 0 potential small deletions
found 0 potential small insertions
>> Performing coverage-search:
Map covers 110216535 bases
Map covers 108217907 bases in sufficiently long segments
Map contains 1983953 good islands
98509451 are left looking bases
98505476 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Examining donor-acceptor pairings in chr1
Examining donor-acceptor pairings in chr2
Examining donor-acceptor pairings in chr3
Examining donor-acceptor pairings in chr4
Examining donor-acceptor pairings in chr5
Examining donor-acceptor pairings in chr6
Examining donor-acceptor pairings in chr7
found 4066401 potential junctions
Reported 4066401 total potential splices
Reporting 0 potential deletions...
Reporting 0 potential insertions...
Reporting potential fusions...

[fabrice]

cat tophat.log

[2013-11-01 17:39:45] Beginning TopHat run (v2.0.9)
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[2013-11-01 17:39:45] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-11-01 17:39:45] Checking for Samtools
Samtools version: 0.1.19.0
[2013-11-01 17:39:45] Checking for Bowtie index files (genome)..
[2013-11-01 17:39:45] Checking for reference FASTA file
[2013-11-01 17:39:45] Generating SAM header for /home/fabrice/genome/bowtie/human/hg19
format: fastq
quality scale: phred33 (default)
[2013-11-01 17:40:15] Preparing reads
left reads: min. length=12, max. length=41, 32543791 kept reads (935808 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
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
[2013-11-01 17:56:46] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-11-01 18:09:16] Searching for junctions via segment mapping
[2013-11-01 18:42:05] Retrieving sequences for splices
[2013-11-01 18:44:37] Indexing splices
[2013-11-02 21:57:29] Mapping left_kept_reads_unmapped to genome segment_juncs with Bowtie2 (1/1)
[2013-11-04 06:42:31] Joining segment hits
[2013-11-04 06:50:16] Reporting output tracks
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[2013-11-04 07:46:44] A summary of the alignment counts can be found in /home/fabrice/projects/analysis/tophat/align_summary.txt
[2013-11-04 07:46:44] Run complete: 2 days 14:06:58 elapsed