[2014-05-29 03:55:15] Beginning TopHat run (v2.0.8b)
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[2014-05-29 03:55:15] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 03:55:15] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 03:55:15] Checking for Bowtie index files
[2014-05-29 03:55:15] Checking for reference FASTA file
[2014-05-29 03:55:15] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 03:55:18] Preparing reads
	 left reads: min. length=60, max. length=101, 36598858 kept reads (506 discarded)
[2014-05-29 04:12:12] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 05:03:35] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 05:08:25] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 05:14:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 05:20:51] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 05:27:36] Searching for junctions via segment mapping
[2014-05-29 05:33:35] Retrieving sequences for splices
[2014-05-29 05:35:34] Indexing splices
[2014-05-29 05:37:01] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 05:39:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 05:43:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 05:46:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 05:49:14] Joining segment hits
[2014-05-29 05:53:40] Reporting output tracks
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[2014-05-29 06:12:59] Run complete: 02:17:44 elapsed