[2019-07-05 11:18:21] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:18:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:18:22] Checking for Bowtie index files (genome)..
[2019-07-05 11:18:22] Checking for reference FASTA file
[2019-07-05 11:18:22] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:18:24] Reading known junctions from GTF file
[2019-07-05 11:18:27] Preparing reads
	 left reads: min. length=150, max. length=150, 21739010 kept reads (1937 discarded)
	right reads: min. length=150, max. length=150, 21726171 kept reads (14776 discarded)
[2019-07-05 12:01:00] Building transcriptome data files /scratch/7534473.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 12:01:19] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 12:08:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:37:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 13:33:04] Resuming TopHat pipeline with unmapped reads
[2019-07-05 13:33:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:49:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:51:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:52:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:54:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:56:04] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:57:43] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:59:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 14:40:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 14:46:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 14:51:17] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 14:56:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 15:01:32] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 15:06:26] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 15:10:54] Searching for junctions via segment mapping
[2019-07-05 19:15:58] Retrieving sequences for splices
[2019-07-05 19:18:08] Indexing splices
[2019-07-05 19:20:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 19:22:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 19:23:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 19:25:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 19:27:07] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 19:28:38] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 19:29:56] Joining segment hits
[2019-07-05 19:36:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 19:40:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 19:45:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 19:49:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 19:54:25] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 19:58:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 20:02:20] Joining segment hits
[2019-07-05 20:14:09] Reporting output tracks
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[2019-07-05 23:11:18] A summary of the alignment counts can be found in /scratch/7534473.1.linga/tophat2/align_summary.txt
[2019-07-05 23:11:18] Run complete: 11:52:57 elapsed