[2014-05-27 10:32:39] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-05-27 10:32:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 10:32:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 10:32:39] Checking for Bowtie index files
[2014-05-27 10:32:39] Checking for reference FASTA file
[2014-05-27 10:32:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 10:32:52] Preparing reads
	 left reads: min. length=60, max. length=101, 24904245 kept reads (1553 discarded)
[2014-05-27 10:42:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 11:21:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 11:24:14] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 11:26:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 11:29:52] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 11:33:05] Searching for junctions via segment mapping
[2014-05-27 11:37:27] Retrieving sequences for splices
[2014-05-27 11:39:31] Indexing splices
[2014-05-27 11:40:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 11:41:24] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 11:43:14] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 11:44:56] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 11:46:26] Joining segment hits
[2014-05-27 11:50:14] Reporting output tracks
-----------------------------------------------
[2014-05-27 12:04:27] Run complete: 01:31:47 elapsed