[2018-10-13 16:07:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:07:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:07:53] Checking for Bowtie index files (genome)..
[2018-10-13 16:07:53] Checking for reference FASTA file
[2018-10-13 16:07:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:07:55] Reading known junctions from GTF file
[2018-10-13 16:07:57] Preparing reads
	 left reads: min. length=100, max. length=100, 451600 kept reads (412 discarded)
	right reads: min. length=100, max. length=100, 451582 kept reads (430 discarded)
[2018-10-13 16:08:10] Building transcriptome data files /scratch/8793345.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:08:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:13:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:13:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:13:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:13:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:14:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:14:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:14:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:14:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:14:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:14:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:14:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:14:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:14:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:15:02] Searching for junctions via segment mapping
[2018-10-13 16:16:32] Retrieving sequences for splices
[2018-10-13 16:17:38] Indexing splices
[2018-10-13 16:17:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:17:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:17:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:17:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:17:58] Joining segment hits
[2018-10-13 16:19:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:19:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:19:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:19:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:19:21] Joining segment hits
[2018-10-13 16:20:34] Reporting output tracks
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[2018-10-13 16:22:48] A summary of the alignment counts can be found in /scratch/8793345.1.p8/tophat2/align_summary.txt
[2018-10-13 16:22:48] Run complete: 00:14:54 elapsed