[2019-09-04 11:15:22] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:15:22] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:15:23] Checking for Bowtie index files (genome)..
[2019-09-04 11:15:23] Checking for reference FASTA file
[2019-09-04 11:15:23] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:15:27] Reading known junctions from GTF file
[2019-09-04 11:15:29] Preparing reads
	 left reads: min. length=150, max. length=150, 29637145 kept reads (13 discarded)
	right reads: min. length=150, max. length=150, 29636070 kept reads (1088 discarded)
[2019-09-04 11:32:18] Building transcriptome data files /scratch/9142563.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:32:26] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:36:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 11:55:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:12:53] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:13:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 12:41:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 12:45:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 12:49:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 12:53:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 12:58:04] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:01:33] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:03:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:32:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:36:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:40:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:44:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:49:06] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:52:56] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:55:01] Searching for junctions via segment mapping
[2019-09-04 14:05:08] Retrieving sequences for splices
[2019-09-04 14:06:09] Indexing splices
[2019-09-04 14:06:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:07:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:08:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:08:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:09:42] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:10:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:10:52] Joining segment hits
[2019-09-04 14:14:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:15:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:15:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:16:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:17:30] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:18:16] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:18:50] Joining segment hits
[2019-09-04 14:22:10] Reporting output tracks
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[2019-09-04 14:42:25] A summary of the alignment counts can be found in /scratch/9142563.1.p16/tophat2/align_summary.txt
[2019-09-04 14:42:25] Run complete: 03:27:02 elapsed