[2014-05-30 00:13:09] Beginning TopHat run (v2.0.8b)
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[2014-05-30 00:13:09] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-30 00:13:09] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-30 00:13:09] Checking for Bowtie index files
[2014-05-30 00:13:09] Checking for reference FASTA file
[2014-05-30 00:13:09] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-30 00:13:11] Preparing reads
	 left reads: min. length=60, max. length=101, 33906302 kept reads (688 discarded)
[2014-05-30 00:27:11] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-30 01:08:37] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-30 01:12:41] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-30 01:16:59] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-30 01:21:30] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-30 01:26:06] Searching for junctions via segment mapping
[2014-05-30 01:31:24] Retrieving sequences for splices
[2014-05-30 01:33:22] Indexing splices
[2014-05-30 01:34:27] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-30 01:36:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-30 01:39:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-30 01:42:51] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-30 01:45:22] Joining segment hits
[2014-05-30 01:49:17] Reporting output tracks
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[2014-05-30 02:05:21] Run complete: 01:52:12 elapsed