[2014-05-27 10:32:40] Beginning TopHat run (v2.0.8b)
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[2014-05-27 10:32:40] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 10:32:40] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 10:32:40] Checking for Bowtie index files
[2014-05-27 10:32:40] Checking for reference FASTA file
[2014-05-27 10:32:40] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 10:32:52] Preparing reads
	 left reads: min. length=60, max. length=101, 28906570 kept reads (736 discarded)
[2014-05-27 10:44:35] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 11:28:29] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 11:31:30] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 11:35:11] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 11:39:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 11:42:57] Searching for junctions via segment mapping
[2014-05-27 11:48:17] Retrieving sequences for splices
[2014-05-27 11:50:25] Indexing splices
[2014-05-27 11:51:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 11:52:37] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 11:54:43] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 11:56:51] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 11:58:44] Joining segment hits
[2014-05-27 12:02:22] Reporting output tracks
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[2014-05-27 12:17:29] Run complete: 01:44:49 elapsed