[2014-04-29 23:14:04] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-04-29 23:14:04] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 23:14:04] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 23:14:04] Checking for Bowtie index files
[2014-04-29 23:14:04] Checking for reference FASTA file
[2014-04-29 23:14:04] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 23:14:07] Preparing reads
	 left reads: min. length=60, max. length=101, 20341411 kept reads (11227 discarded)
[2014-04-29 23:22:06] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 23:46:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 23:50:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 23:53:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 23:57:00] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 00:00:47] Searching for junctions via segment mapping
[2014-04-30 00:58:01] Retrieving sequences for splices
[2014-04-30 00:59:57] Indexing splices
[2014-04-30 01:00:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 01:08:47] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 01:16:23] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 01:24:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 01:33:14] Joining segment hits
[2014-04-30 01:41:17] Reporting output tracks
-----------------------------------------------
[2014-04-30 01:52:49] Run complete: 02:38:45 elapsed