[2019-07-03 17:28:22] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:28:22] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:28:23] Checking for Bowtie index files (genome)..
[2019-07-03 17:28:23] Checking for reference FASTA file
[2019-07-03 17:28:23] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:28:27] Reading known junctions from GTF file
[2019-07-03 17:28:30] Preparing reads
	 left reads: min. length=150, max. length=150, 32924899 kept reads (450 discarded)
	right reads: min. length=150, max. length=150, 32925272 kept reads (77 discarded)
[2019-07-03 18:02:18] Building transcriptome data files /scratch/7505698.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:02:35] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:09:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:32:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:57:43] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:57:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:05:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:17:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:29:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:42:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:54:06] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 21:02:07] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:05:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 22:10:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 22:24:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:37:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:50:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 23:04:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 23:13:38] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 23:18:27] Searching for junctions via segment mapping
[2019-07-04 10:05:00] Retrieving sequences for splices
[2019-07-04 10:08:06] Indexing splices
[2019-07-04 10:09:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 10:25:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 10:40:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 10:52:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 11:03:08] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 11:09:42] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 11:11:13] Joining segment hits
[2019-07-04 11:29:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 11:41:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 11:52:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 12:03:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 12:14:08] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 12:20:31] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 12:22:14] Joining segment hits
[2019-07-04 12:41:02] Reporting output tracks
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[2019-07-04 13:59:45] A summary of the alignment counts can be found in /scratch/7505698.1.linga/tophat2/align_summary.txt
[2019-07-04 13:59:45] Run complete: 20:31:23 elapsed