[2014-05-29 08:23:27] Beginning TopHat run (v2.0.8b)
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[2014-05-29 08:23:27] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 08:23:27] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 08:23:27] Checking for Bowtie index files
[2014-05-29 08:23:27] Checking for reference FASTA file
[2014-05-29 08:23:27] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 08:23:30] Preparing reads
	 left reads: min. length=60, max. length=101, 29814809 kept reads (155 discarded)
[2014-05-29 08:38:14] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 09:22:00] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 09:26:31] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 09:31:20] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 09:36:20] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 09:41:43] Searching for junctions via segment mapping
[2014-05-29 09:47:21] Retrieving sequences for splices
[2014-05-29 09:49:18] Indexing splices
[2014-05-29 09:50:24] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 09:52:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 09:55:32] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 09:58:28] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 10:01:08] Joining segment hits
[2014-05-29 10:06:06] Reporting output tracks
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[2014-05-29 10:23:32] Run complete: 02:00:05 elapsed