[2014-05-28 11:55:47] Beginning TopHat run (v2.0.8b)
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[2014-05-28 11:55:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 11:55:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 11:55:48] Checking for Bowtie index files
[2014-05-28 11:55:48] Checking for reference FASTA file
[2014-05-28 11:55:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 11:56:01] Preparing reads
	 left reads: min. length=60, max. length=101, 23504266 kept reads (2414 discarded)
[2014-05-28 12:05:43] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 12:43:22] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 12:45:50] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 12:48:35] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 12:51:28] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 12:54:44] Searching for junctions via segment mapping
[2014-05-28 13:01:57] Retrieving sequences for splices
[2014-05-28 13:04:05] Indexing splices
[2014-05-28 13:05:07] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 13:06:52] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 13:08:57] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 13:11:01] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 13:12:57] Joining segment hits
[2014-05-28 13:17:05] Reporting output tracks
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[2014-05-28 13:31:35] Run complete: 01:35:47 elapsed