[2014-05-29 07:30:42] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-29 07:30:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 07:30:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 07:30:42] Checking for Bowtie index files
[2014-05-29 07:30:42] Checking for reference FASTA file
[2014-05-29 07:30:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 07:30:45] Preparing reads
	 left reads: min. length=60, max. length=101, 24680611 kept reads (2541 discarded)
[2014-05-29 07:41:55] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 08:15:55] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 08:22:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 08:28:20] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 08:33:36] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 08:39:45] Searching for junctions via segment mapping
[2014-05-29 09:48:58] Retrieving sequences for splices
[2014-05-29 09:50:57] Indexing splices
[2014-05-29 09:52:01] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 10:11:17] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 10:28:45] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 10:45:36] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 11:06:19] Joining segment hits
[2014-05-29 11:16:41] Reporting output tracks
-----------------------------------------------
[2014-05-29 11:29:30] Run complete: 03:58:47 elapsed