[2019-07-04 04:17:57] Beginning TopHat run (v2.1.1)
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[2019-07-04 04:17:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-04 04:17:57] Checking for Bowtie index files (genome)..
[2019-07-04 04:17:57] Checking for reference FASTA file
[2019-07-04 04:17:57] Generating SAM header for Bowtie2Index/genome
[2019-07-04 04:17:59] Reading known junctions from GTF file
[2019-07-04 04:18:01] Preparing reads
	 left reads: min. length=150, max. length=150, 34586084 kept reads (443 discarded)
	right reads: min. length=150, max. length=150, 34586445 kept reads (82 discarded)
[2019-07-04 04:39:05] Building transcriptome data files /scratch/7505716.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 04:39:14] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 04:43:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 04:59:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 05:16:02] Resuming TopHat pipeline with unmapped reads
[2019-07-04 05:16:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 05:49:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 05:54:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 06:00:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 06:06:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 06:11:51] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 06:16:00] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 06:18:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 06:53:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 06:59:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 07:05:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 07:12:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 07:18:57] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 07:23:35] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 07:26:29] Searching for junctions via segment mapping
[2019-07-04 10:47:40] Retrieving sequences for splices
[2019-07-04 10:48:50] Indexing splices
[2019-07-04 10:49:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 10:53:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 10:57:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 11:02:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 11:06:41] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 11:09:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 11:10:25] Joining segment hits
[2019-07-04 11:17:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 11:22:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 11:26:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 11:31:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 11:35:15] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 11:37:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 11:38:58] Joining segment hits
[2019-07-04 11:46:00] Reporting output tracks
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[2019-07-04 12:13:51] A summary of the alignment counts can be found in /scratch/7505716.1.p16/tophat2/align_summary.txt
[2019-07-04 12:13:51] Run complete: 07:55:53 elapsed