[2014-05-28 04:22:17] Beginning TopHat run (v2.0.8b)
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[2014-05-28 04:22:17] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 04:22:17] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 04:22:17] Checking for Bowtie index files
[2014-05-28 04:22:17] Checking for reference FASTA file
[2014-05-28 04:22:17] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 04:22:20] Preparing reads
	 left reads: min. length=60, max. length=101, 27430919 kept reads (2681 discarded)
[2014-05-28 04:34:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 05:13:13] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 05:16:13] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 05:19:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 05:23:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 05:26:46] Searching for junctions via segment mapping
[2014-05-28 05:36:05] Retrieving sequences for splices
[2014-05-28 05:38:12] Indexing splices
[2014-05-28 05:39:10] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 05:43:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 05:48:22] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 05:53:06] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 05:58:10] Joining segment hits
[2014-05-28 06:03:53] Reporting output tracks
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[2014-05-28 06:21:47] Run complete: 01:59:29 elapsed