[2014-05-28 04:58:50] Beginning TopHat run (v2.0.8b)
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[2014-05-28 04:58:50] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 04:58:50] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 04:58:50] Checking for Bowtie index files
[2014-05-28 04:58:50] Checking for reference FASTA file
[2014-05-28 04:58:50] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 04:58:53] Preparing reads
	 left reads: min. length=60, max. length=101, 56658405 kept reads (8945 discarded)
[2014-05-28 05:24:49] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 07:08:10] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 07:33:23] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 07:58:28] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 08:23:32] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 08:51:01] Searching for junctions via segment mapping
[2014-05-28 19:15:54] Retrieving sequences for splices
[2014-05-28 19:18:01] Indexing splices
[2014-05-28 19:21:01] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 20:13:55] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 21:07:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 22:02:43] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 22:57:31] Joining segment hits
[2014-05-28 23:12:59] Reporting output tracks
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[2014-05-28 23:47:37] Run complete: 18:48:46 elapsed