[2014-05-09 23:06:24] Beginning TopHat run (v2.0.8b)
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[2014-05-09 23:06:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-09 23:06:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-09 23:06:24] Checking for Bowtie index files
[2014-05-09 23:06:24] Checking for reference FASTA file
[2014-05-09 23:06:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-09 23:06:26] Preparing reads
	 left reads: min. length=60, max. length=101, 22096278 kept reads (3614 discarded)
[2014-05-09 23:15:24] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-09 23:40:15] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-09 23:42:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-09 23:44:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-09 23:46:51] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-09 23:49:05] Searching for junctions via segment mapping
[2014-05-09 23:52:33] Retrieving sequences for splices
[2014-05-09 23:54:28] Indexing splices
[2014-05-09 23:55:08] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-09 23:56:06] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-09 23:57:17] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-09 23:58:28] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-09 23:59:26] Joining segment hits
[2014-05-10 00:02:27] Reporting output tracks
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[2014-05-10 00:13:40] Run complete: 01:07:16 elapsed