[2019-09-04 15:17:33] Beginning TopHat run (v2.1.1)
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[2019-09-04 15:17:33] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 15:17:33] Checking for Bowtie index files (genome)..
[2019-09-04 15:17:33] Checking for reference FASTA file
[2019-09-04 15:17:33] Generating SAM header for Bowtie2Index/genome
[2019-09-04 15:17:43] Reading known junctions from GTF file
[2019-09-04 15:17:46] Preparing reads
	 left reads: min. length=150, max. length=150, 29120814 kept reads (7 discarded)
	right reads: min. length=150, max. length=150, 29119753 kept reads (1068 discarded)
[2019-09-04 15:34:45] Building transcriptome data files /scratch/9142573.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 15:34:55] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 15:39:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 16:03:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 16:25:02] Resuming TopHat pipeline with unmapped reads
[2019-09-04 16:25:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:50:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:54:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 16:58:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 17:02:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 17:05:50] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 17:08:52] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 17:10:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 17:36:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 17:39:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 17:43:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 17:47:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 17:51:04] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 17:54:28] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 17:56:16] Searching for junctions via segment mapping
[2019-09-04 18:03:16] Retrieving sequences for splices
[2019-09-04 18:04:18] Indexing splices
[2019-09-04 18:04:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 18:05:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 18:06:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 18:07:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 18:08:02] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 18:08:41] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 18:09:07] Joining segment hits
[2019-09-04 18:12:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 18:13:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 18:13:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 18:14:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 18:15:09] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 18:15:51] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 18:16:23] Joining segment hits
[2019-09-04 18:19:41] Reporting output tracks
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[2019-09-04 18:38:27] A summary of the alignment counts can be found in /scratch/9142573.1.p16/tophat2/align_summary.txt
[2019-09-04 18:38:27] Run complete: 03:20:54 elapsed