[2014-05-28 18:21:13] Beginning TopHat run (v2.0.8b)
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[2014-05-28 18:21:13] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 18:21:13] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 18:21:13] Checking for Bowtie index files
[2014-05-28 18:21:13] Checking for reference FASTA file
[2014-05-28 18:21:13] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 18:21:15] Preparing reads
	 left reads: min. length=60, max. length=101, 23541143 kept reads (215 discarded)
[2014-05-28 18:32:34] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 19:08:24] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 19:11:01] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 19:14:02] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 19:17:06] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 19:19:51] Searching for junctions via segment mapping
[2014-05-28 19:24:05] Retrieving sequences for splices
[2014-05-28 19:26:03] Indexing splices
[2014-05-28 19:26:50] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 19:28:14] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 19:29:58] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 19:31:43] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 19:33:16] Joining segment hits
[2014-05-28 19:36:33] Reporting output tracks
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[2014-05-28 19:50:32] Run complete: 01:29:18 elapsed