[2014-05-28 18:15:12] Beginning TopHat run (v2.0.8b)
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[2014-05-28 18:15:12] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 18:15:12] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 18:15:12] Checking for Bowtie index files
[2014-05-28 18:15:12] Checking for reference FASTA file
[2014-05-28 18:15:12] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 18:15:14] Preparing reads
	 left reads: min. length=60, max. length=101, 29423457 kept reads (427 discarded)
[2014-05-28 18:28:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 19:22:24] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 19:35:07] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 19:48:13] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 20:01:36] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 20:16:22] Searching for junctions via segment mapping
[2014-05-29 01:41:06] Retrieving sequences for splices
[2014-05-29 01:43:19] Indexing splices
[2014-05-29 01:44:57] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 02:10:22] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 02:36:50] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 03:02:44] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 03:26:51] Joining segment hits
[2014-05-29 03:35:33] Reporting output tracks
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[2014-05-29 03:54:44] Run complete: 09:39:32 elapsed