[2019-06-28 13:26:34] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:34] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:34] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:34] Checking for reference FASTA file
[2019-06-28 13:26:34] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:37] Reading known junctions from GTF file
[2019-06-28 13:26:41] Preparing reads
	 left reads: min. length=150, max. length=150, 23625019 kept reads (477 discarded)
	right reads: min. length=150, max. length=150, 23625385 kept reads (111 discarded)
[2019-06-28 13:54:18] Building transcriptome data files /scratch/7287275.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:54:36] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:01:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:22:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:45:42] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:45:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:32:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:37:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:43:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:49:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:55:29] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:59:57] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:02:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:51:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:57:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:03:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:10:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:16:28] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:22:06] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:25:24] Searching for junctions via segment mapping
[2019-06-28 20:15:56] Retrieving sequences for splices
[2019-06-28 20:18:38] Indexing splices
[2019-06-28 20:19:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:22:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:25:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:28:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:31:30] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:33:50] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:34:46] Joining segment hits
[2019-06-28 20:44:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:48:52] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:52:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:56:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:59:47] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 21:02:23] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 21:03:35] Joining segment hits
[2019-06-28 21:13:57] Reporting output tracks
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[2019-06-28 22:18:48] A summary of the alignment counts can be found in /scratch/7287275.1.linga/tophat2/align_summary.txt
[2019-06-28 22:18:48] Run complete: 08:52:14 elapsed