[2019-06-28 13:26:31] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:31] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:31] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:31] Checking for reference FASTA file
[2019-06-28 13:26:31] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:35] Reading known junctions from GTF file
[2019-06-28 13:26:39] Preparing reads
	 left reads: min. length=150, max. length=150, 20527588 kept reads (327 discarded)
	right reads: min. length=150, max. length=150, 20527822 kept reads (93 discarded)
[2019-06-28 13:51:31] Building transcriptome data files /scratch/7287265.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:51:52] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 13:59:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:24:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 15:03:18] Resuming TopHat pipeline with unmapped reads
[2019-06-28 15:03:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:42:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:49:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:58:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:06:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:15:44] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:21:44] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:23:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:05:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:13:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:21:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:30:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:39:28] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:46:23] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:49:28] Searching for junctions via segment mapping
[2019-06-29 03:26:41] Retrieving sequences for splices
[2019-06-29 03:29:51] Indexing splices
[2019-06-29 03:31:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 03:39:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 03:47:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 03:55:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 04:03:38] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 04:09:46] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 04:11:22] Joining segment hits
[2019-06-29 04:25:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 04:33:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 04:41:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 04:48:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 04:56:04] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 05:01:30] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 05:02:57] Joining segment hits
[2019-06-29 05:18:12] Reporting output tracks
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[2019-06-29 06:48:17] A summary of the alignment counts can be found in /scratch/7287265.1.linga/tophat2/align_summary.txt
[2019-06-29 06:48:17] Run complete: 17:21:46 elapsed