[2018-10-13 06:15:17] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:15:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:15:17] Checking for Bowtie index files (genome)..
[2018-10-13 06:15:17] Checking for reference FASTA file
[2018-10-13 06:15:17] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:15:19] Reading known junctions from GTF file
[2018-10-13 06:15:21] Preparing reads
	 left reads: min. length=100, max. length=100, 550551 kept reads (156 discarded)
	right reads: min. length=100, max. length=100, 550391 kept reads (316 discarded)
[2018-10-13 06:15:34] Building transcriptome data files /scratch/8793051.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:15:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:20:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:20:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:21:29] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:21:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:21:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:21:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:21:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:21:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:22:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:22:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:22:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:22:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:22:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:22:40] Searching for junctions via segment mapping
[2018-10-13 06:25:12] Retrieving sequences for splices
[2018-10-13 06:26:22] Indexing splices
[2018-10-13 06:26:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:26:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:26:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:26:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:26:46] Joining segment hits
[2018-10-13 06:28:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:28:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:28:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:28:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:28:13] Joining segment hits
[2018-10-13 06:29:27] Reporting output tracks
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[2018-10-13 06:36:16] A summary of the alignment counts can be found in /scratch/8793051.1.p8/tophat2/align_summary.txt
[2018-10-13 06:36:16] Run complete: 00:20:58 elapsed