[2014-04-30 01:52:49] Beginning TopHat run (v2.0.8b)
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[2014-04-30 01:52:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 01:52:49] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 01:52:49] Checking for Bowtie index files
[2014-04-30 01:52:49] Checking for reference FASTA file
[2014-04-30 01:52:49] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 01:52:52] Preparing reads
	 left reads: min. length=60, max. length=101, 19306195 kept reads (9897 discarded)
[2014-04-30 02:00:41] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 02:24:16] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 02:26:09] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 02:28:14] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 02:30:41] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 02:33:13] Searching for junctions via segment mapping
[2014-04-30 02:37:05] Retrieving sequences for splices
[2014-04-30 02:39:08] Indexing splices
[2014-04-30 02:39:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 02:40:42] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 02:41:55] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 02:43:08] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 02:44:20] Joining segment hits
[2014-04-30 02:47:43] Reporting output tracks
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[2014-04-30 02:59:32] Run complete: 01:06:43 elapsed