[2014-05-29 11:26:52] Beginning TopHat run (v2.0.8b)
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[2014-05-29 11:26:52] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 11:26:52] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 11:26:52] Checking for Bowtie index files
[2014-05-29 11:26:52] Checking for reference FASTA file
[2014-05-29 11:26:52] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 11:26:54] Preparing reads
	 left reads: min. length=60, max. length=101, 25611383 kept reads (1555 discarded)
[2014-05-29 11:38:39] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 12:18:31] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 12:25:03] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 12:30:47] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 12:36:33] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 12:42:45] Searching for junctions via segment mapping
[2014-05-29 13:38:44] Retrieving sequences for splices
[2014-05-29 13:40:54] Indexing splices
[2014-05-29 13:41:50] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 13:58:40] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 14:14:51] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 14:30:37] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 14:47:35] Joining segment hits
[2014-05-29 14:55:45] Reporting output tracks
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[2014-05-29 15:10:57] Run complete: 03:44:04 elapsed