[2018-10-13 14:15:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:15:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:15:29] Checking for Bowtie index files (genome)..
[2018-10-13 14:15:29] Checking for reference FASTA file
[2018-10-13 14:15:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:15:31] Reading known junctions from GTF file
[2018-10-13 14:15:34] Preparing reads
	 left reads: min. length=100, max. length=100, 327544 kept reads (182 discarded)
	right reads: min. length=100, max. length=100, 327309 kept reads (417 discarded)
[2018-10-13 14:15:44] Building transcriptome data files /scratch/8793282.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:15:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:20:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:21:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:21:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:21:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:21:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:21:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:21:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:21:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:21:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:22:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:22:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:22:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:22:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:22:20] Searching for junctions via segment mapping
[2018-10-13 14:23:46] Retrieving sequences for splices
[2018-10-13 14:25:05] Indexing splices
[2018-10-13 14:25:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:25:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:25:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:25:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:25:25] Joining segment hits
[2018-10-13 14:26:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:26:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:26:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:26:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:26:48] Joining segment hits
[2018-10-13 14:28:01] Reporting output tracks
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[2018-10-13 14:29:59] A summary of the alignment counts can be found in /scratch/8793282.1.p8/tophat2/align_summary.txt
[2018-10-13 14:29:59] Run complete: 00:14:30 elapsed