[2014-05-29 02:01:02] Beginning TopHat run (v2.0.8b)
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[2014-05-29 02:01:02] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 02:01:02] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 02:01:02] Checking for Bowtie index files
[2014-05-29 02:01:02] Checking for reference FASTA file
[2014-05-29 02:01:02] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 02:01:05] Preparing reads
	 left reads: min. length=60, max. length=101, 19759528 kept reads (588 discarded)
[2014-05-29 02:10:09] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 02:37:51] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 02:40:18] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 02:42:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 02:45:36] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 02:49:21] Searching for junctions via segment mapping
[2014-05-29 02:55:26] Retrieving sequences for splices
[2014-05-29 02:57:35] Indexing splices
[2014-05-29 02:58:07] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 03:01:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 03:05:14] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 03:08:50] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 03:12:41] Joining segment hits
[2014-05-29 03:17:56] Reporting output tracks
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[2014-05-29 03:29:19] Run complete: 01:28:16 elapsed