[2019-07-03 17:35:22] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:35:22] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:35:22] Checking for Bowtie index files (genome)..
[2019-07-03 17:35:22] Checking for reference FASTA file
[2019-07-03 17:35:22] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:35:24] Reading known junctions from GTF file
[2019-07-03 17:35:26] Preparing reads
	 left reads: min. length=150, max. length=150, 30064645 kept reads (421 discarded)
	right reads: min. length=150, max. length=150, 30064973 kept reads (93 discarded)
[2019-07-03 17:53:47] Building transcriptome data files /scratch/7505701.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 17:53:56] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 17:58:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:14:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:31:10] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:31:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 18:59:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:04:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 19:10:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 19:16:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 19:21:42] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 19:25:21] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 19:27:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:57:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:03:05] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:09:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:16:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:22:54] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:27:21] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:30:04] Searching for junctions via segment mapping
[2019-07-04 02:05:11] Retrieving sequences for splices
[2019-07-04 02:06:21] Indexing splices
[2019-07-04 02:06:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:12:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:17:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:23:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 02:28:12] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 02:31:37] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 02:32:45] Joining segment hits
[2019-07-04 02:40:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:46:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:51:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:57:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 03:02:35] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 03:05:50] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 03:07:01] Joining segment hits
[2019-07-04 03:15:05] Reporting output tracks
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[2019-07-04 03:45:23] A summary of the alignment counts can be found in /scratch/7505701.1.p16/tophat2/align_summary.txt
[2019-07-04 03:45:23] Run complete: 10:10:00 elapsed