[2014-05-28 01:57:29] Beginning TopHat run (v2.0.8b)
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[2014-05-28 01:57:29] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 01:57:29] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 01:57:29] Checking for Bowtie index files
[2014-05-28 01:57:29] Checking for reference FASTA file
[2014-05-28 01:57:29] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 01:57:32] Preparing reads
	 left reads: min. length=60, max. length=101, 26203234 kept reads (1820 discarded)
[2014-05-28 02:09:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 02:57:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 03:01:17] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 03:05:24] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 03:09:39] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 03:14:06] Searching for junctions via segment mapping
[2014-05-28 03:29:59] Retrieving sequences for splices
[2014-05-28 03:32:06] Indexing splices
[2014-05-28 03:33:08] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 03:38:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 03:44:56] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 03:51:01] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 03:57:11] Joining segment hits
[2014-05-28 04:04:40] Reporting output tracks
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[2014-05-28 04:22:17] Run complete: 02:24:47 elapsed