[2014-04-28 12:18:57] Beginning TopHat run (v2.0.8b)
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[2014-04-28 12:18:57] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 12:18:57] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 12:18:57] Checking for Bowtie index files
[2014-04-28 12:18:57] Checking for reference FASTA file
[2014-04-28 12:18:57] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 12:19:12] Preparing reads
	 left reads: min. length=60, max. length=101, 19731142 kept reads (9750 discarded)
[2014-04-28 12:27:09] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 12:53:50] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 12:55:55] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 12:58:13] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 13:02:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 13:05:08] Searching for junctions via segment mapping
[2014-04-28 13:08:46] Retrieving sequences for splices
[2014-04-28 13:10:43] Indexing splices
[2014-04-28 13:11:25] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 13:12:13] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 13:13:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 13:14:12] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 13:15:08] Joining segment hits
[2014-04-28 13:18:28] Reporting output tracks
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[2014-04-28 13:29:51] Run complete: 01:10:54 elapsed