[2019-07-17 19:14:24] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:14:24] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:26] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:26] Checking for reference FASTA file
[2019-07-17 19:14:26] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:32] Reading known junctions from GTF file
[2019-07-17 19:14:35] Preparing reads
	 left reads: min. length=150, max. length=150, 63997098 kept reads (5841 discarded)
	right reads: min. length=150, max. length=150, 63987140 kept reads (15799 discarded)
[2019-07-17 20:18:56] Building transcriptome data files /scratch/7775059.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:19:15] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:25:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:19:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:17:11] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:17:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:58:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:14:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:31:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:48:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 01:05:35] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:18:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:24:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 03:29:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 03:48:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 04:06:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 04:25:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 04:43:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 04:59:34] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 05:08:12] Searching for junctions via segment mapping
[2019-07-18 21:52:55] Retrieving sequences for splices
[2019-07-18 21:55:25] Indexing splices
[2019-07-18 21:57:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 22:11:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 22:25:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 22:40:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 22:54:41] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 23:04:56] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 23:08:36] Joining segment hits
[2019-07-18 23:38:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 23:54:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 00:09:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 00:25:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 00:41:04] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 00:51:04] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 00:53:37] Joining segment hits
[2019-07-19 01:21:06] Reporting output tracks
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[2019-07-19 03:36:24] A summary of the alignment counts can be found in /scratch/7775059.1.linga/tophat2/align_summary.txt
[2019-07-19 03:36:24] Run complete: 1 days 08:21:59 elapsed