[2019-09-04 11:22:30] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:22:30] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:22:30] Checking for Bowtie index files (genome)..
[2019-09-04 11:22:30] Checking for reference FASTA file
[2019-09-04 11:22:30] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:22:35] Reading known junctions from GTF file
[2019-09-04 11:22:39] Preparing reads
	 left reads: min. length=150, max. length=150, 27881320 kept reads (12 discarded)
	right reads: min. length=150, max. length=150, 27880300 kept reads (1032 discarded)
[2019-09-04 11:48:48] Building transcriptome data files /scratch/9142568.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:49:05] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:56:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 15:23:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 18:21:57] Resuming TopHat pipeline with unmapped reads
[2019-09-04 18:21:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 20:25:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 20:45:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 21:06:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 21:27:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 21:46:47] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 22:02:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 22:11:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 23:39:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 23:54:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-05 00:10:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-05 00:27:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-05 00:44:52] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-05 01:00:47] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-05 01:10:11] Searching for junctions via segment mapping
[2019-09-05 01:34:45] Retrieving sequences for splices
[2019-09-05 01:36:38] Indexing splices
[2019-09-05 01:37:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-05 01:46:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-05 01:55:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-05 02:04:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-05 02:12:14] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-05 02:18:49] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-05 02:22:29] Joining segment hits
[2019-09-05 02:38:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-05 02:42:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-05 02:47:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-05 02:52:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-05 02:59:49] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-05 03:06:28] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-05 03:12:08] Joining segment hits
[2019-09-05 03:26:20] Reporting output tracks
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[2019-09-05 04:18:12] A summary of the alignment counts can be found in /scratch/9142568.1.linga/tophat2/align_summary.txt
[2019-09-05 04:18:12] Run complete: 16:55:42 elapsed