[2019-06-28 13:26:34] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:34] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:34] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:34] Checking for reference FASTA file
[2019-06-28 13:26:34] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:39] Reading known junctions from GTF file
[2019-06-28 13:26:44] Preparing reads
	 left reads: min. length=150, max. length=150, 23114007 kept reads (408 discarded)
	right reads: min. length=150, max. length=150, 23114302 kept reads (113 discarded)
[2019-06-28 13:52:11] Building transcriptome data files /scratch/7287274.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:52:29] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 13:59:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:22:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:46:49] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:46:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:34:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:39:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:46:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:53:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:59:52] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:05:56] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:08:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:57:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:03:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:10:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:18:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:25:47] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:31:19] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:34:35] Searching for junctions via segment mapping
[2019-06-28 22:10:46] Retrieving sequences for splices
[2019-06-28 22:13:23] Indexing splices
[2019-06-28 22:14:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 22:18:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 22:22:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 22:26:34] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 22:30:40] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 22:33:54] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 22:34:57] Joining segment hits
[2019-06-28 22:45:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 22:49:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 22:53:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 22:58:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 23:02:11] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 23:05:16] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 23:06:18] Joining segment hits
[2019-06-28 23:16:49] Reporting output tracks
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[2019-06-29 00:15:46] A summary of the alignment counts can be found in /scratch/7287274.1.linga/tophat2/align_summary.txt
[2019-06-29 00:15:46] Run complete: 10:49:12 elapsed