[2019-07-12 13:53:10] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:53:10] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:53:10] Checking for Bowtie index files (genome)..
[2019-07-12 13:53:10] Checking for reference FASTA file
[2019-07-12 13:53:10] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:53:12] Reading known junctions from GTF file
[2019-07-12 13:53:14] Preparing reads
	 left reads: min. length=151, max. length=151, 64763953 kept reads (115 discarded)
	right reads: min. length=151, max. length=151, 64757108 kept reads (6960 discarded)
[2019-07-12 14:39:04] Building transcriptome data files /scratch/7678213.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:39:13] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:43:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:20:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:58:44] Resuming TopHat pipeline with unmapped reads
[2019-07-12 15:58:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 17:07:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 17:18:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 17:29:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 17:41:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 17:52:13] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 18:01:31] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 18:09:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:23:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:35:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 19:47:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 19:59:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 20:11:38] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 20:21:15] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 20:30:51] Searching for junctions via segment mapping
[2019-07-12 20:56:34] Retrieving sequences for splices
[2019-07-12 20:57:44] Indexing splices
[2019-07-12 20:58:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 21:02:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 21:07:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 21:11:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 21:16:04] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 21:19:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 21:21:56] Joining segment hits
[2019-07-12 21:30:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 21:35:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 21:40:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 21:45:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 21:49:47] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 21:53:22] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 21:56:10] Joining segment hits
[2019-07-12 22:04:59] Reporting output tracks
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[2019-07-12 22:54:21] A summary of the alignment counts can be found in /scratch/7678213.1.p/tophat2/align_summary.txt
[2019-07-12 22:54:21] Run complete: 09:01:10 elapsed