[2019-06-28 13:24:58] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:24:58] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:24:59] Checking for Bowtie index files (genome)..
[2019-06-28 13:24:59] Checking for reference FASTA file
[2019-06-28 13:24:59] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:25:05] Reading known junctions from GTF file
[2019-06-28 13:25:09] Preparing reads
	 left reads: min. length=150, max. length=150, 23459836 kept reads (537 discarded)
	right reads: min. length=150, max. length=150, 23460284 kept reads (89 discarded)
[2019-06-28 13:51:57] Building transcriptome data files /scratch/7287272.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:52:16] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 13:59:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:16:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:34:14] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:34:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:18:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:22:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:26:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:31:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:35:30] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:39:12] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 15:41:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:28:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:33:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:38:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:42:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:47:43] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:51:51] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:54:17] Searching for junctions via segment mapping
[2019-06-28 19:54:52] Retrieving sequences for splices
[2019-06-28 19:57:23] Indexing splices
[2019-06-28 19:58:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:01:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:04:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:07:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:10:54] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:13:24] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:14:20] Joining segment hits
[2019-06-28 20:23:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:26:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:30:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:33:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:36:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:39:32] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:40:26] Joining segment hits
[2019-06-28 20:49:52] Reporting output tracks
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[2019-06-28 21:41:40] A summary of the alignment counts can be found in /scratch/7287272.1.linga/tophat2/align_summary.txt
[2019-06-28 21:41:40] Run complete: 08:16:41 elapsed