[2014-05-28 21:04:28] Beginning TopHat run (v2.0.8b)
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[2014-05-28 21:04:28] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 21:04:28] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 21:04:28] Checking for Bowtie index files
[2014-05-28 21:04:28] Checking for reference FASTA file
[2014-05-28 21:04:28] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 21:04:30] Preparing reads
	 left reads: min. length=60, max. length=101, 23435428 kept reads (1074 discarded)
[2014-05-28 21:15:30] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 21:55:29] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 22:01:45] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 22:07:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 22:13:12] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 22:19:21] Searching for junctions via segment mapping
[2014-05-28 23:14:13] Retrieving sequences for splices
[2014-05-28 23:16:21] Indexing splices
[2014-05-28 23:17:13] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 23:33:57] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 23:48:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 00:01:45] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 00:19:00] Joining segment hits
[2014-05-29 00:28:15] Reporting output tracks
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[2014-05-29 00:42:13] Run complete: 03:37:45 elapsed