[2014-04-29 18:07:21] Beginning TopHat run (v2.0.8b)
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[2014-04-29 18:07:21] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 18:07:21] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 18:07:21] Checking for Bowtie index files
[2014-04-29 18:07:21] Checking for reference FASTA file
[2014-04-29 18:07:21] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 18:07:23] Preparing reads
	 left reads: min. length=60, max. length=101, 22064338 kept reads (9948 discarded)
[2014-04-29 18:16:21] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 18:43:56] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 18:46:22] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 18:49:08] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 18:54:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 18:57:03] Searching for junctions via segment mapping
[2014-04-29 19:01:11] Retrieving sequences for splices
[2014-04-29 19:03:08] Indexing splices
[2014-04-29 19:03:43] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 19:04:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 19:06:12] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 19:07:36] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 19:08:57] Joining segment hits
[2014-04-29 19:12:55] Reporting output tracks
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[2014-04-29 19:26:58] Run complete: 01:19:37 elapsed