[2014-05-29 03:21:40] Beginning TopHat run (v2.0.8b)
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[2014-05-29 03:21:40] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 03:21:40] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 03:21:40] Checking for Bowtie index files
[2014-05-29 03:21:40] Checking for reference FASTA file
[2014-05-29 03:21:40] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 03:21:43] Preparing reads
	 left reads: min. length=60, max. length=101, 21875414 kept reads (1380 discarded)
[2014-05-29 03:31:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 04:04:04] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 04:06:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 04:09:30] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 04:12:32] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 04:16:17] Searching for junctions via segment mapping
[2014-05-29 04:24:22] Retrieving sequences for splices
[2014-05-29 04:26:32] Indexing splices
[2014-05-29 04:27:26] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 04:30:15] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 04:33:25] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 04:36:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 04:39:44] Joining segment hits
[2014-05-29 04:44:25] Reporting output tracks
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[2014-05-29 04:58:46] Run complete: 01:37:05 elapsed