[2019-06-28 13:25:23] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:25:23] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:25:24] Checking for Bowtie index files (genome)..
[2019-06-28 13:25:24] Checking for reference FASTA file
[2019-06-28 13:25:24] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:25:29] Reading known junctions from GTF file
[2019-06-28 13:25:33] Preparing reads
	 left reads: min. length=150, max. length=150, 23367931 kept reads (406 discarded)
	right reads: min. length=150, max. length=150, 23368241 kept reads (96 discarded)
[2019-06-28 13:54:05] Building transcriptome data files /scratch/7287269.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:54:26] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:02:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:32:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 15:05:39] Resuming TopHat pipeline with unmapped reads
[2019-06-28 15:05:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:47:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:53:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:59:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:07:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:15:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:21:17] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:23:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:12:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:19:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:25:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:33:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:42:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:48:47] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:52:09] Searching for junctions via segment mapping
[2019-06-29 01:00:43] Retrieving sequences for splices
[2019-06-29 01:03:17] Indexing splices
[2019-06-29 01:04:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 01:09:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 01:15:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 01:21:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 01:27:17] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 01:31:37] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 01:32:49] Joining segment hits
[2019-06-29 01:44:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 01:51:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 01:57:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 02:03:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 02:09:22] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 02:13:50] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 02:15:08] Joining segment hits
[2019-06-29 02:28:55] Reporting output tracks
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[2019-06-29 03:30:00] A summary of the alignment counts can be found in /scratch/7287269.1.linga/tophat2/align_summary.txt
[2019-06-29 03:30:00] Run complete: 14:04:36 elapsed