[2014-05-27 19:03:11] Beginning TopHat run (v2.0.8b)
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[2014-05-27 19:03:11] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 19:03:11] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 19:03:11] Checking for Bowtie index files
[2014-05-27 19:03:11] Checking for reference FASTA file
[2014-05-27 19:03:11] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 19:03:13] Preparing reads
	 left reads: min. length=60, max. length=101, 26983163 kept reads (1361 discarded)
[2014-05-27 19:15:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 19:59:14] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 20:03:04] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 20:07:06] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 20:11:26] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 20:16:07] Searching for junctions via segment mapping
[2014-05-27 20:22:00] Retrieving sequences for splices
[2014-05-27 20:24:09] Indexing splices
[2014-05-27 20:24:44] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 20:28:28] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 20:32:37] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 20:36:35] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 20:40:46] Joining segment hits
[2014-05-27 20:45:43] Reporting output tracks
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[2014-05-27 21:01:44] Run complete: 01:58:33 elapsed