[2018-10-13 18:20:19] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:20:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:20:19] Checking for Bowtie index files (genome)..
[2018-10-13 18:20:19] Checking for reference FASTA file
[2018-10-13 18:20:19] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:20:21] Reading known junctions from GTF file
[2018-10-13 18:20:24] Preparing reads
	 left reads: min. length=100, max. length=100, 489635 kept reads (142 discarded)
	right reads: min. length=100, max. length=100, 489322 kept reads (455 discarded)
[2018-10-13 18:20:38] Building transcriptome data files /scratch/8793434.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:20:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:25:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:26:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:26:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:26:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:26:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:26:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:26:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:27:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:27:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:27:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:27:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:27:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:27:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:27:46] Searching for junctions via segment mapping
[2018-10-13 18:29:12] Retrieving sequences for splices
[2018-10-13 18:30:18] Indexing splices
[2018-10-13 18:30:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:30:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:30:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:30:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:30:37] Joining segment hits
[2018-10-13 18:31:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:31:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:31:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:32:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:32:02] Joining segment hits
[2018-10-13 18:33:17] Reporting output tracks
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[2018-10-13 18:35:10] A summary of the alignment counts can be found in /scratch/8793434.1.p8/tophat2/align_summary.txt
[2018-10-13 18:35:10] Run complete: 00:14:50 elapsed