[2019-07-05 15:03:18] Beginning TopHat run (v2.1.1)
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[2019-07-05 15:03:18] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 15:03:18] Checking for Bowtie index files (genome)..
[2019-07-05 15:03:18] Checking for reference FASTA file
[2019-07-05 15:03:18] Generating SAM header for Bowtie2Index/genome
[2019-07-05 15:03:20] Reading known junctions from GTF file
[2019-07-05 15:03:22] Preparing reads
	 left reads: min. length=150, max. length=150, 24950576 kept reads (1791 discarded)
	right reads: min. length=150, max. length=150, 24933462 kept reads (18905 discarded)
[2019-07-05 15:19:45] Building transcriptome data files /scratch/7534491.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 15:19:54] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 15:24:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:37:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:50:52] Resuming TopHat pipeline with unmapped reads
[2019-07-05 15:50:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 15:58:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 15:59:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 16:00:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 16:00:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 16:01:36] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 16:02:18] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 16:03:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 16:12:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 16:13:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 16:14:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 16:15:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 16:16:35] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 16:17:33] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 16:18:29] Searching for junctions via segment mapping
[2019-07-05 16:44:13] Retrieving sequences for splices
[2019-07-05 16:45:24] Indexing splices
[2019-07-05 16:45:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:46:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:46:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:47:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:47:29] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:47:52] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:48:14] Joining segment hits
[2019-07-05 16:50:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:51:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:51:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:52:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:52:40] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:53:09] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:53:37] Joining segment hits
[2019-07-05 16:56:03] Reporting output tracks
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[2019-07-05 17:22:07] A summary of the alignment counts can be found in /scratch/7534491.1.p8/tophat2/align_summary.txt
[2019-07-05 17:22:07] Run complete: 02:18:49 elapsed