[2014-05-27 10:32:39] Beginning TopHat run (v2.0.8b)
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[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, 26800201 kept reads (637 discarded)
[2014-05-27 10:43:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 11:25:48] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 11:29:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 11:32:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 11:35:29] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 11:38:39] Searching for junctions via segment mapping
[2014-05-27 11:44:13] Retrieving sequences for splices
[2014-05-27 11:46:18] Indexing splices
[2014-05-27 11:46:59] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 11:48:25] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 11:50:19] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 11:52:04] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 11:53:31] Joining segment hits
[2014-05-27 11:57:02] Reporting output tracks
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[2014-05-27 12:10:48] Run complete: 01:38:09 elapsed