[2018-10-13 14:04:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:04:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:04:31] Checking for Bowtie index files (genome)..
[2018-10-13 14:04:31] Checking for reference FASTA file
[2018-10-13 14:04:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:04:33] Reading known junctions from GTF file
[2018-10-13 14:04:37] Preparing reads
	 left reads: min. length=100, max. length=100, 849273 kept reads (121 discarded)
	right reads: min. length=100, max. length=100, 849122 kept reads (272 discarded)
[2018-10-13 14:05:01] Building transcriptome data files /scratch/8793279.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:05:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:09:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:10:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:10:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:10:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:11:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:11:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:11:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:11:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:11:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:11:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:12:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:12:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:12:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:12:18] Searching for junctions via segment mapping
[2018-10-13 14:14:45] Retrieving sequences for splices
[2018-10-13 14:15:51] Indexing splices
[2018-10-13 14:16:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:16:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:16:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:16:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:16:14] Joining segment hits
[2018-10-13 14:17:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:17:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:17:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:17:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:17:42] Joining segment hits
[2018-10-13 14:18:58] Reporting output tracks
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[2018-10-13 14:25:07] A summary of the alignment counts can be found in /scratch/8793279.1.p16/tophat2/align_summary.txt
[2018-10-13 14:25:07] Run complete: 00:20:36 elapsed