[2014-05-29 03:29:25] Beginning TopHat run (v2.0.8b)
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[2014-05-29 03:29:25] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 03:29:25] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 03:29:25] Checking for Bowtie index files
[2014-05-29 03:29:25] Checking for reference FASTA file
[2014-05-29 03:29:25] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 03:29:27] Preparing reads
	 left reads: min. length=60, max. length=101, 29893002 kept reads (326 discarded)
[2014-05-29 03:44:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 04:29:19] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 04:33:49] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 04:38:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 04:43:47] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 04:49:04] Searching for junctions via segment mapping
[2014-05-29 04:54:24] Retrieving sequences for splices
[2014-05-29 04:56:35] Indexing splices
[2014-05-29 04:57:52] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 05:00:01] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 05:02:38] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 05:05:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 05:07:36] Joining segment hits
[2014-05-29 05:11:36] Reporting output tracks
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[2014-05-29 05:28:39] Run complete: 01:59:13 elapsed