[2014-05-27 10:32:38] Beginning TopHat run (v2.0.8b)
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[2014-05-27 10:32:38] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 10:32:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 10:32:39] Checking for Bowtie index files
[2014-05-27 10:32:39] Checking for reference FASTA file
[2014-05-27 10:32:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 10:32:44] Preparing reads
	 left reads: min. length=60, max. length=101, 25942249 kept reads (887 discarded)
[2014-05-27 10:44:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 11:30:03] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 11:32:44] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 11:35:20] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 11:38:34] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 11:42:12] Searching for junctions via segment mapping
[2014-05-27 11:47:11] Retrieving sequences for splices
[2014-05-27 11:49:16] Indexing splices
[2014-05-27 11:49:56] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 11:51:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 11:54:02] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 11:56:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 11:58:26] Joining segment hits
[2014-05-27 12:02:38] Reporting output tracks
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[2014-05-27 12:19:12] Run complete: 01:46:33 elapsed