[2014-05-04 13:06:58] Beginning TopHat run (v2.0.8b)
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[2014-05-04 13:06:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-04 13:06:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-04 13:06:58] Checking for Bowtie index files
[2014-05-04 13:06:58] Checking for reference FASTA file
[2014-05-04 13:06:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-04 13:07:01] Preparing reads
	 left reads: min. length=60, max. length=101, 25935284 kept reads (6200 discarded)
[2014-05-04 13:17:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-04 13:57:56] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-04 14:07:20] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-04 14:16:57] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-04 14:26:05] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-04 14:36:55] Searching for junctions via segment mapping
[2014-05-04 23:37:06] Retrieving sequences for splices
[2014-05-04 23:39:02] Indexing splices
[2014-05-04 23:40:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-04 23:55:46] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 00:11:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 00:26:50] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 00:42:41] Joining segment hits
[2014-05-05 00:55:01] Reporting output tracks
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[2014-05-05 01:13:22] Run complete: 12:06:24 elapsed