[2018-10-13 17:15:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:15:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:15:53] Checking for Bowtie index files (genome)..
[2018-10-13 17:15:53] Checking for reference FASTA file
[2018-10-13 17:15:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:15:55] Reading known junctions from GTF file
[2018-10-13 17:15:57] Preparing reads
	 left reads: min. length=100, max. length=100, 413587 kept reads (167 discarded)
	right reads: min. length=100, max. length=100, 413359 kept reads (395 discarded)
[2018-10-13 17:16:07] Building transcriptome data files /scratch/8793390.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:16:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:20:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:21:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:21:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:21:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:21:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:21:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:22:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:22:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:22:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:22:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:22:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:22:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:22:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:22:46] Searching for junctions via segment mapping
[2018-10-13 17:24:12] Retrieving sequences for splices
[2018-10-13 17:25:19] Indexing splices
[2018-10-13 17:25:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:25:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:25:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:25:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:25:38] Joining segment hits
[2018-10-13 17:26:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:26:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:26:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:26:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:26:57] Joining segment hits
[2018-10-13 17:28:07] Reporting output tracks
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[2018-10-13 17:30:06] A summary of the alignment counts can be found in /scratch/8793390.1.p16/tophat2/align_summary.txt
[2018-10-13 17:30:07] Run complete: 00:14:13 elapsed