[2014-05-29 12:36:03] Beginning TopHat run (v2.0.8b)
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[2014-05-29 12:36:03] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 12:36:03] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 12:36:03] Checking for Bowtie index files
[2014-05-29 12:36:03] Checking for reference FASTA file
[2014-05-29 12:36:03] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 12:36:06] Preparing reads
	 left reads: min. length=60, max. length=101, 27244587 kept reads (669 discarded)
[2014-05-29 12:48:56] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 13:28:05] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 13:31:10] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 13:34:16] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 13:37:04] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 13:40:35] Searching for junctions via segment mapping
[2014-05-29 13:45:50] Retrieving sequences for splices
[2014-05-29 13:47:57] Indexing splices
[2014-05-29 13:48:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 13:50:11] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 13:51:55] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 13:53:38] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 13:55:04] Joining segment hits
[2014-05-29 13:59:25] Reporting output tracks
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[2014-05-29 14:15:30] Run complete: 01:39:26 elapsed