[2019-07-12 13:38:10] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:38:10] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:38:10] Checking for Bowtie index files (genome)..
[2019-07-12 13:38:10] Checking for reference FASTA file
[2019-07-12 13:38:10] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:38:12] Reading known junctions from GTF file
[2019-07-12 13:38:14] Preparing reads
	 left reads: min. length=151, max. length=151, 74128011 kept reads (153 discarded)
	right reads: min. length=151, max. length=151, 74120430 kept reads (7734 discarded)
[2019-07-12 14:30:02] Building transcriptome data files /scratch/7678209.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:30:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:34:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:00:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:28:59] Resuming TopHat pipeline with unmapped reads
[2019-07-12 15:28:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 16:48:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 17:03:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 17:17:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 17:32:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 17:46:15] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 17:58:00] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 18:09:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:50:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:05:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 20:21:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 20:36:36] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 20:49:38] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 21:03:06] Searching for junctions via segment mapping
[2019-07-12 21:25:50] Retrieving sequences for splices
[2019-07-12 21:27:00] Indexing splices
[2019-07-12 21:27:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 21:57:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 22:28:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 22:58:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 23:27:18] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 23:51:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 00:06:24] Joining segment hits
[2019-07-13 00:41:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 01:12:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 01:44:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 02:15:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 02:45:38] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 03:10:27] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 03:27:37] Joining segment hits
[2019-07-13 04:05:16] Reporting output tracks
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[2019-07-13 04:55:58] A summary of the alignment counts can be found in /scratch/7678209.1.p16/tophat2/align_summary.txt
[2019-07-13 04:55:58] Run complete: 15:17:48 elapsed