[2014-05-05 11:29:01] Beginning TopHat run (v2.0.8b)
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[2014-05-05 11:29:01] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 11:29:01] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 11:29:01] Checking for Bowtie index files
[2014-05-05 11:29:01] Checking for reference FASTA file
[2014-05-05 11:29:01] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 11:29:03] Preparing reads
	 left reads: min. length=60, max. length=101, 25378443 kept reads (5759 discarded)
[2014-05-05 11:39:15] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 12:10:00] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 12:13:21] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 12:16:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 12:21:14] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 12:25:02] Searching for junctions via segment mapping
[2014-05-05 12:32:32] Retrieving sequences for splices
[2014-05-05 12:34:28] Indexing splices
[2014-05-05 12:35:02] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 12:38:01] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 12:41:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 12:44:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 12:47:41] Joining segment hits
[2014-05-05 12:54:22] Reporting output tracks
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[2014-05-05 13:10:16] Run complete: 01:41:15 elapsed