[2019-09-04 15:28:46] Beginning TopHat run (v2.1.1)
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[2019-09-04 15:28:46] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 15:28:48] Checking for Bowtie index files (genome)..
[2019-09-04 15:28:48] Checking for reference FASTA file
[2019-09-04 15:28:48] Generating SAM header for Bowtie2Index/genome
[2019-09-04 15:28:49] Reading known junctions from GTF file
[2019-09-04 15:28:52] Preparing reads
	 left reads: min. length=150, max. length=150, 19783458 kept reads (7 discarded)
	right reads: min. length=150, max. length=150, 19782716 kept reads (749 discarded)
[2019-09-04 15:39:45] Building transcriptome data files /scratch/9142575.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 15:40:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 15:44:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 16:38:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 17:32:59] Resuming TopHat pipeline with unmapped reads
[2019-09-04 17:32:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 18:11:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 18:16:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 18:22:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 18:28:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 18:33:23] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 18:37:33] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 18:39:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 19:18:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 19:23:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 19:29:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 19:34:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 19:40:33] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 19:45:07] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 19:47:47] Searching for junctions via segment mapping
[2019-09-04 19:58:35] Retrieving sequences for splices
[2019-09-04 19:59:38] Indexing splices
[2019-09-04 20:00:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 20:01:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 20:03:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 20:04:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 20:06:30] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 20:07:52] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 20:08:48] Joining segment hits
[2019-09-04 20:13:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 20:14:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 20:15:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 20:17:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 20:19:02] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 20:20:33] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 20:21:41] Joining segment hits
[2019-09-04 20:26:18] Reporting output tracks
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[2019-09-04 20:45:37] A summary of the alignment counts can be found in /scratch/9142575.1.p16/tophat2/align_summary.txt
[2019-09-04 20:45:37] Run complete: 05:16:50 elapsed