[2014-05-29 02:33:24] Beginning TopHat run (v2.0.8b)
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[2014-05-29 02:33:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 02:33:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 02:33:24] Checking for Bowtie index files
[2014-05-29 02:33:24] Checking for reference FASTA file
[2014-05-29 02:33:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 02:33:26] Preparing reads
	 left reads: min. length=60, max. length=101, 27729271 kept reads (2989 discarded)
[2014-05-29 02:45:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 03:29:47] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 03:37:13] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 03:44:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 03:53:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 04:04:05] Searching for junctions via segment mapping
[2014-05-29 07:07:35] Retrieving sequences for splices
[2014-05-29 07:09:32] Indexing splices
[2014-05-29 07:10:35] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 07:25:37] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 07:40:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 07:55:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 08:10:28] Joining segment hits
[2014-05-29 08:19:05] Reporting output tracks
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[2014-05-29 08:37:03] Run complete: 06:03:38 elapsed