[2019-07-05 14:26:02] Beginning TopHat run (v2.1.1)
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[2019-07-05 14:26:02] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 14:26:02] Checking for Bowtie index files (genome)..
[2019-07-05 14:26:02] Checking for reference FASTA file
[2019-07-05 14:26:02] Generating SAM header for Bowtie2Index/genome
[2019-07-05 14:26:03] Reading known junctions from GTF file
[2019-07-05 14:26:05] Preparing reads
	 left reads: min. length=150, max. length=150, 22472391 kept reads (1554 discarded)
	right reads: min. length=150, max. length=150, 22456928 kept reads (17017 discarded)
[2019-07-05 14:40:53] Building transcriptome data files /scratch/7534489.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 14:41:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 14:45:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:00:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:15:29] Resuming TopHat pipeline with unmapped reads
[2019-07-05 15:15:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 15:22:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 15:23:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 15:23:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 15:24:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 15:25:02] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 15:25:42] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 15:26:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 15:34:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 15:35:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 15:36:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 15:37:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 15:38:34] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 15:39:29] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 15:40:21] Searching for junctions via segment mapping
[2019-07-05 16:17:36] Retrieving sequences for splices
[2019-07-05 16:18:45] Indexing splices
[2019-07-05 16:19:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:19:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:20:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:20:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:21:14] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:21:40] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:22:03] Joining segment hits
[2019-07-05 16:24:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:25:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:25:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:26:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:26:57] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:27:32] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:28:02] Joining segment hits
[2019-07-05 16:30:34] Reporting output tracks
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[2019-07-05 17:04:13] A summary of the alignment counts can be found in /scratch/7534489.1.p16/tophat2/align_summary.txt
[2019-07-05 17:04:13] Run complete: 02:38:11 elapsed