[2014-05-05 20:52:44] Beginning TopHat run (v2.0.8b)
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[2014-05-05 20:52:44] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 20:52:44] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 20:52:44] Checking for Bowtie index files
[2014-05-05 20:52:44] Checking for reference FASTA file
[2014-05-05 20:52:44] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 20:52:50] Preparing reads
	 left reads: min. length=60, max. length=101, 24814136 kept reads (5082 discarded)
[2014-05-05 21:03:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 21:32:11] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 21:35:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 21:38:01] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 21:41:13] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 21:44:57] Searching for junctions via segment mapping
[2014-05-05 21:52:01] Retrieving sequences for splices
[2014-05-05 21:53:58] Indexing splices
[2014-05-05 21:54:29] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 21:57:00] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 21:59:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 22:02:28] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 22:05:20] Joining segment hits
[2014-05-05 22:11:11] Reporting output tracks
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[2014-05-05 22:27:58] Run complete: 01:35:14 elapsed