[2019-09-04 12:10:45] Beginning TopHat run (v2.1.1)
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[2019-09-04 12:10:45] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 12:11:07] Checking for Bowtie index files (genome)..
[2019-09-04 12:11:07] Checking for reference FASTA file
[2019-09-04 12:11:07] Generating SAM header for Bowtie2Index/genome
[2019-09-04 12:11:17] Reading known junctions from GTF file
[2019-09-04 12:11:22] Preparing reads
	 left reads: min. length=150, max. length=150, 32215995 kept reads (9 discarded)
	right reads: min. length=150, max. length=150, 32214808 kept reads (1196 discarded)
[2019-09-04 12:30:10] Building transcriptome data files /scratch/9142571.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 12:30:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 12:35:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:25:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 14:10:57] Resuming TopHat pipeline with unmapped reads
[2019-09-04 14:10:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:50:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:56:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:02:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:09:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:15:01] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:19:51] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:22:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:00:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:06:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 16:12:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:18:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:24:14] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:29:29] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:32:28] Searching for junctions via segment mapping
[2019-09-04 16:41:56] Retrieving sequences for splices
[2019-09-04 16:43:00] Indexing splices
[2019-09-04 16:43:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:45:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 16:46:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 16:48:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 16:50:17] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 16:51:40] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 16:52:30] Joining segment hits
[2019-09-04 16:57:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:58:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:00:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:01:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:02:51] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:04:13] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:05:17] Joining segment hits
[2019-09-04 17:09:58] Reporting output tracks
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[2019-09-04 17:36:03] A summary of the alignment counts can be found in /scratch/9142571.1.p8/tophat2/align_summary.txt
[2019-09-04 17:36:03] Run complete: 05:25:17 elapsed