[2014-04-27 03:57:14] Beginning TopHat run (v2.0.8b)
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[2014-04-27 03:57:14] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 03:57:14] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 03:57:14] Checking for Bowtie index files
[2014-04-27 03:57:14] Checking for reference FASTA file
[2014-04-27 03:57:14] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 03:57:17] Preparing reads
	 left reads: min. length=60, max. length=101, 22805906 kept reads (10626 discarded)
[2014-04-27 04:06:30] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 04:35:19] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 04:38:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 04:41:06] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 04:46:52] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 04:50:14] Searching for junctions via segment mapping
[2014-04-27 04:55:38] Retrieving sequences for splices
[2014-04-27 04:57:34] Indexing splices
[2014-04-27 04:58:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 04:59:44] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 05:01:13] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 05:02:46] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 05:04:11] Joining segment hits
[2014-04-27 05:08:00] Reporting output tracks
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[2014-04-27 05:20:53] Run complete: 01:23:38 elapsed