[2019-07-13 00:36:45] Beginning TopHat run (v2.1.1)
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[2019-07-13 00:36:45] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-13 00:36:45] Checking for Bowtie index files (genome)..
[2019-07-13 00:36:45] Checking for reference FASTA file
[2019-07-13 00:36:45] Generating SAM header for Bowtie2Index/genome
[2019-07-13 00:36:46] Reading known junctions from GTF file
[2019-07-13 00:36:48] Preparing reads
	 left reads: min. length=150, max. length=150, 62071591 kept reads (5431 discarded)
	right reads: min. length=150, max. length=150, 62061678 kept reads (15344 discarded)
[2019-07-13 01:17:11] Building transcriptome data files /scratch/7682059.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-07-13 01:17:21] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-13 01:21:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 01:59:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 02:37:04] Resuming TopHat pipeline with unmapped reads
[2019-07-13 02:37:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 03:25:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 03:32:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:40:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:48:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 03:56:09] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 04:02:10] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 04:05:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 04:55:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 05:03:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 05:12:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 05:20:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 05:28:46] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:35:10] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:39:19] Searching for junctions via segment mapping
[2019-07-13 12:53:55] Retrieving sequences for splices
[2019-07-13 12:55:11] Indexing splices
[2019-07-13 12:55:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 13:01:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 13:08:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 13:14:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 13:21:04] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 13:25:46] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 13:27:35] Joining segment hits
[2019-07-13 13:37:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 13:44:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 13:51:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 13:57:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 14:04:08] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 14:08:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 14:10:18] Joining segment hits
[2019-07-13 14:19:42] Reporting output tracks
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[2019-07-13 15:27:05] A summary of the alignment counts can be found in /scratch/7682059.1.c/tophat2/align_summary.txt
[2019-07-13 15:27:05] Run complete: 14:50:20 elapsed