[2019-07-03 17:41:42] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:41:42] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:41:43] Checking for Bowtie index files (genome)..
[2019-07-03 17:41:43] Checking for reference FASTA file
[2019-07-03 17:41:43] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:41:44] Reading known junctions from GTF file
[2019-07-03 17:41:46] Preparing reads
	 left reads: min. length=150, max. length=150, 30066168 kept reads (467 discarded)
	right reads: min. length=150, max. length=150, 30066549 kept reads (86 discarded)
[2019-07-03 18:00:27] Building transcriptome data files /scratch/7505702.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:00:36] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:05:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:21:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:36:50] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:36:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:04:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:10:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 19:15:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 19:21:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 19:26:39] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 19:30:25] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 19:32:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:01:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:07:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:13:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:19:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:25:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:29:26] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:32:06] Searching for junctions via segment mapping
[2019-07-04 00:29:44] Retrieving sequences for splices
[2019-07-04 00:30:55] Indexing splices
[2019-07-04 00:31:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 00:35:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 00:39:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 00:43:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 00:47:57] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 00:50:33] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 00:51:28] Joining segment hits
[2019-07-04 00:57:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 01:02:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 01:06:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 01:11:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 01:15:07] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 01:17:43] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 01:18:41] Joining segment hits
[2019-07-04 01:25:33] Reporting output tracks
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[2019-07-04 01:57:02] A summary of the alignment counts can be found in /scratch/7505702.1.p16/tophat2/align_summary.txt
[2019-07-04 01:57:02] Run complete: 08:15:19 elapsed