[2019-09-04 11:15:29] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:15:29] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:15:30] Checking for Bowtie index files (genome)..
[2019-09-04 11:15:30] Checking for reference FASTA file
[2019-09-04 11:15:30] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:15:31] Reading known junctions from GTF file
[2019-09-04 11:15:34] Preparing reads
	 left reads: min. length=150, max. length=150, 32813603 kept reads (6 discarded)
	right reads: min. length=150, max. length=150, 32812343 kept reads (1266 discarded)
[2019-09-04 11:34:48] Building transcriptome data files /scratch/9142565.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:34:58] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:39:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:31:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:18:38] Resuming TopHat pipeline with unmapped reads
[2019-09-04 13:18:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:59:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:05:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:11:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:17:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:22:53] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:27:42] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:30:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 15:08:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:13:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:18:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:24:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:29:35] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:34:27] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:37:18] Searching for junctions via segment mapping
[2019-09-04 15:46:20] Retrieving sequences for splices
[2019-09-04 15:47:26] Indexing splices
[2019-09-04 15:47:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 15:49:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 15:51:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 15:52:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 15:54:14] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 15:55:36] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 15:56:24] Joining segment hits
[2019-09-04 16:01:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 16:02:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 16:03:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 16:04:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 16:05:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 16:07:11] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 16:08:12] Joining segment hits
[2019-09-04 16:12:42] Reporting output tracks
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[2019-09-04 16:37:57] A summary of the alignment counts can be found in /scratch/9142565.1.c/tophat2/align_summary.txt
[2019-09-04 16:37:57] Run complete: 05:22:27 elapsed