[2018-10-13 15:40:38] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:40:38] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:40:38] Checking for Bowtie index files (genome)..
[2018-10-13 15:40:38] Checking for reference FASTA file
[2018-10-13 15:40:38] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:40:40] Reading known junctions from GTF file
[2018-10-13 15:40:43] Preparing reads
	 left reads: min. length=100, max. length=100, 264595 kept reads (172 discarded)
	right reads: min. length=100, max. length=100, 264440 kept reads (327 discarded)
[2018-10-13 15:40:50] Building transcriptome data files /scratch/8793326.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:41:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:45:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:45:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:46:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:46:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:46:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:46:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:46:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:46:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:46:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:46:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:46:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:46:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:47:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:47:05] Searching for junctions via segment mapping
[2018-10-13 15:48:25] Retrieving sequences for splices
[2018-10-13 15:49:32] Indexing splices
[2018-10-13 15:49:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:49:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:49:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:49:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:49:50] Joining segment hits
[2018-10-13 15:50:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:51:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:51:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:51:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:51:08] Joining segment hits
[2018-10-13 15:52:16] Reporting output tracks
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[2018-10-13 15:54:02] A summary of the alignment counts can be found in /scratch/8793326.1.p16/tophat2/align_summary.txt
[2018-10-13 15:54:02] Run complete: 00:13:23 elapsed