[2014-05-28 19:25:39] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-28 19:25:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 19:25:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 19:25:39] Checking for Bowtie index files
[2014-05-28 19:25:39] Checking for reference FASTA file
[2014-05-28 19:25:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 19:25:41] Preparing reads
	 left reads: min. length=60, max. length=101, 28611154 kept reads (3798 discarded)
[2014-05-28 19:38:20] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 20:28:38] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 20:37:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 20:46:24] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 20:56:08] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 21:07:11] Searching for junctions via segment mapping
[2014-05-29 00:56:08] Retrieving sequences for splices
[2014-05-29 00:58:13] Indexing splices
[2014-05-29 00:59:27] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 01:16:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 01:34:06] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 01:51:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 02:06:52] Joining segment hits
[2014-05-29 02:14:52] Reporting output tracks
-----------------------------------------------
[2014-05-29 02:33:24] Run complete: 07:07:44 elapsed