[2014-04-26 04:49:08] Beginning TopHat run (v2.0.8b)
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[2014-04-26 04:49:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 04:49:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 04:49:08] Checking for Bowtie index files
[2014-04-26 04:49:08] Checking for reference FASTA file
[2014-04-26 04:49:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 04:49:10] Preparing reads
	 left reads: min. length=60, max. length=101, 22673135 kept reads (17651 discarded)
[2014-04-26 04:58:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 05:28:07] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 05:30:25] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 05:33:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 05:35:56] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 05:38:49] Searching for junctions via segment mapping
[2014-04-26 05:46:25] Retrieving sequences for splices
[2014-04-26 05:48:21] Indexing splices
[2014-04-26 05:49:01] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 05:50:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 05:51:34] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 05:52:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 05:54:18] Joining segment hits
[2014-04-26 05:57:53] Reporting output tracks
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[2014-04-26 06:11:22] Run complete: 01:22:14 elapsed