segment_juncs v1.0.13
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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
Loading left segment hits...	Processed 500000 root segment groups
Microaligned 0 segments
done.
Loading right segment hits...	Processed 500000 root segment groups
Microaligned 0 segments
done.
Found 3028601 potential split-segment junctions
Indexing extensions in /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg1_missing.fq
Indexing extensions in /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//left_kept_reads_seg2_missing.fq
Indexing extensions in /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg1_missing.fq
Indexing extensions in /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/tmp//right_kept_reads_seg2_missing.fq
Total extensions: 160457472
Total extensions: 160457472
Total extensions: 160457472
Total extensions: 160457472
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
Adding hits from segment file 2 to coverage map
Adding hits from segment file 3 to coverage map
Map covers 35938613 bases
Map covers 35178405 bases in sufficiently long segments
Map contains 756133 good islands
37678802 are left looking bases
37679024 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Examining donor-acceptor pairings in chr20
Examining donor-acceptor pairings in chr21
Examining donor-acceptor pairings in chr22
Examining donor-acceptor pairings in chr19
Examining donor-acceptor pairings in chr18
Examining donor-acceptor pairings in chr11
Examining donor-acceptor pairings in chr10
Examining donor-acceptor pairings in chr13
Examining donor-acceptor pairings in chr12
Examining donor-acceptor pairings in chr15
Examining donor-acceptor pairings in chr14
Examining donor-acceptor pairings in chr17
Examining donor-acceptor pairings in chr16
Examining donor-acceptor pairings in chrX
Examining donor-acceptor pairings in chrY
Examining donor-acceptor pairings in chrM
Examining donor-acceptor pairings in chr2
Examining donor-acceptor pairings in chr3
Examining donor-acceptor pairings in chr1
Examining donor-acceptor pairings in chr6
Examining donor-acceptor pairings in chr7
Examining donor-acceptor pairings in chr4
Examining donor-acceptor pairings in chr5
Examining donor-acceptor pairings in chr8
Examining donor-acceptor pairings in chr9
Found 1012295 potential island-end pairing junctions
done
Reporting potential splice junctions...done
Reported 3418170 total possible splices