[2019-07-03 17:28:37] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:28:37] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:28:37] Checking for Bowtie index files (genome)..
[2019-07-03 17:28:37] Checking for reference FASTA file
[2019-07-03 17:28:37] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:28:40] Reading known junctions from GTF file
[2019-07-03 17:28:43] Preparing reads
	 left reads: min. length=150, max. length=150, 31194253 kept reads (449 discarded)
	right reads: min. length=150, max. length=150, 31194615 kept reads (87 discarded)
[2019-07-03 17:59:48] Building transcriptome data files /scratch/7505699.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:00:06] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:06:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:30:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:56:57] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:56:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:01:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:12:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:25:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:38:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:50:55] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:59:04] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:02:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 22:11:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 22:25:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:39:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:53:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 23:07:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 23:17:20] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 23:21:49] Searching for junctions via segment mapping
[2019-07-04 13:17:54] Retrieving sequences for splices
[2019-07-04 13:20:40] Indexing splices
[2019-07-04 13:22:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 13:38:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 13:53:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 14:06:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 14:18:12] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 14:26:07] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 14:27:48] Joining segment hits
[2019-07-04 14:49:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 15:02:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 15:16:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 15:29:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 15:41:52] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 15:49:18] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 15:51:06] Joining segment hits
[2019-07-04 16:11:36] Reporting output tracks
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[2019-07-04 17:36:54] A summary of the alignment counts can be found in /scratch/7505699.1.linga/tophat2/align_summary.txt
[2019-07-04 17:36:54] Run complete: 1 days 00:08:17 elapsed