[2014-05-01 04:33:58] Beginning TopHat run (v2.0.8b)
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[2014-05-01 04:33:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-01 04:33:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-01 04:33:58] Checking for Bowtie index files
[2014-05-01 04:33:58] Checking for reference FASTA file
[2014-05-01 04:33:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-01 04:34:00] Preparing reads
	 left reads: min. length=60, max. length=101, 19915987 kept reads (11145 discarded)
[2014-05-01 04:41:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-01 05:13:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-01 05:20:43] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-01 05:27:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-01 05:35:58] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-01 05:43:35] Searching for junctions via segment mapping
[2014-05-01 11:38:44] Retrieving sequences for splices
[2014-05-01 11:40:40] Indexing splices
[2014-05-01 11:41:52] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-01 11:52:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-01 12:02:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-01 12:13:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-01 12:24:03] Joining segment hits
[2014-05-01 12:33:49] Reporting output tracks
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[2014-05-01 12:47:59] Run complete: 08:14:01 elapsed