[2019-07-17 19:14:32] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:14:32] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:36] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:36] Checking for reference FASTA file
[2019-07-17 19:14:36] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:43] Reading known junctions from GTF file
[2019-07-17 19:14:46] Preparing reads
	 left reads: min. length=150, max. length=150, 64818606 kept reads (5780 discarded)
	right reads: min. length=150, max. length=150, 64808291 kept reads (16095 discarded)
[2019-07-17 20:21:53] Building transcriptome data files /scratch/7775062.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:22:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:28:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:17:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:10:50] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:10:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:03:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:16:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:31:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:45:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 00:59:49] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:10:26] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:15:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 03:19:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 03:36:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 03:53:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 04:09:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 04:24:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 04:36:42] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 04:44:06] Searching for junctions via segment mapping
[2019-07-18 16:54:03] Retrieving sequences for splices
[2019-07-18 16:56:40] Indexing splices
[2019-07-18 16:58:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 17:10:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 17:23:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 17:35:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 17:48:18] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 17:57:03] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 17:59:24] Joining segment hits
[2019-07-18 18:22:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 18:35:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 18:47:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 18:59:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 19:10:44] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 19:18:45] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 19:21:06] Joining segment hits
[2019-07-18 19:45:06] Reporting output tracks
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[2019-07-18 22:06:03] A summary of the alignment counts can be found in /scratch/7775062.1.linga/tophat2/align_summary.txt
[2019-07-18 22:06:03] Run complete: 1 days 02:51:30 elapsed