[2014-05-29 15:10:49] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-29 15:10:49] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 15:10:49] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 15:10:49] Checking for Bowtie index files
[2014-05-29 15:10:49] Checking for reference FASTA file
[2014-05-29 15:10:49] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 15:10:51] Preparing reads
	 left reads: min. length=60, max. length=101, 26280956 kept reads (2036 discarded)
[2014-05-29 15:22:23] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 15:56:48] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 16:03:38] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 16:10:49] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 16:17:23] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 16:24:49] Searching for junctions via segment mapping
[2014-05-29 17:29:56] Retrieving sequences for splices
[2014-05-29 17:31:53] Indexing splices
[2014-05-29 17:32:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 17:51:56] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 18:10:27] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 18:27:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 18:46:55] Joining segment hits
[2014-05-29 18:56:07] Reporting output tracks
-----------------------------------------------
[2014-05-29 19:09:33] Run complete: 03:58:44 elapsed