[2014-04-30 08:39:56] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-30 08:39:56] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 08:39:56] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 08:39:56] Checking for Bowtie index files
[2014-04-30 08:39:56] Checking for reference FASTA file
[2014-04-30 08:39:56] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 08:39:59] Preparing reads
	 left reads: min. length=60, max. length=101, 17575017 kept reads (9139 discarded)
[2014-04-30 08:47:07] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 09:09:08] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 09:10:52] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 09:12:48] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 09:15:07] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 09:17:26] Searching for junctions via segment mapping
[2014-04-30 09:22:11] Retrieving sequences for splices
[2014-04-30 09:24:07] Indexing splices
[2014-04-30 09:24:42] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 09:25:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 09:26:32] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 09:27:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 09:28:30] Joining segment hits
[2014-04-30 09:31:37] Reporting output tracks
-----------------------------------------------
[2014-04-30 09:42:20] Run complete: 01:02:23 elapsed