[2014-04-30 07:35:11] Beginning TopHat run (v2.0.8b)
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[2014-04-30 07:35:11] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 07:35:11] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 07:35:11] Checking for Bowtie index files
[2014-04-30 07:35:11] Checking for reference FASTA file
[2014-04-30 07:35:11] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 07:35:13] Preparing reads
	 left reads: min. length=60, max. length=101, 18395943 kept reads (10283 discarded)
[2014-04-30 07:42:38] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 08:05:50] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 08:07:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 08:09:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 08:12:01] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 08:14:24] Searching for junctions via segment mapping
[2014-04-30 08:19:07] Retrieving sequences for splices
[2014-04-30 08:21:03] Indexing splices
[2014-04-30 08:21:37] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 08:22:28] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 08:23:30] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 08:24:32] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 08:25:32] Joining segment hits
[2014-04-30 08:28:41] Reporting output tracks
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[2014-04-30 08:39:56] Run complete: 01:04:45 elapsed