[2014-05-06 00:33:15] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-06 00:33:15] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-06 00:33:15] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-06 00:33:15] Checking for Bowtie index files
[2014-05-06 00:33:15] Checking for reference FASTA file
[2014-05-06 00:33:15] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-06 00:33:39] Preparing reads
	 left reads: min. length=60, max. length=101, 25597519 kept reads (8289 discarded)
[2014-05-06 00:44:25] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-06 01:22:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-06 01:26:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-06 01:30:24] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-06 01:34:07] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-06 01:37:48] Searching for junctions via segment mapping
[2014-05-06 01:52:09] Retrieving sequences for splices
[2014-05-06 01:54:07] Indexing splices
[2014-05-06 01:55:10] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-06 01:57:04] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-06 01:59:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-06 02:01:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-06 02:03:32] Joining segment hits
[2014-05-06 02:10:05] Reporting output tracks
-----------------------------------------------
[2014-05-06 02:28:32] Run complete: 01:55:17 elapsed