[2019-07-03 18:59:49] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:59:49] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:59:49] Checking for Bowtie index files (genome)..
[2019-07-03 18:59:49] Checking for reference FASTA file
[2019-07-03 18:59:49] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:59:51] Reading known junctions from GTF file
[2019-07-03 18:59:54] Preparing reads
	 left reads: min. length=150, max. length=150, 32095590 kept reads (444 discarded)
	right reads: min. length=150, max. length=150, 32095955 kept reads (79 discarded)
[2019-07-03 19:33:32] Building transcriptome data files /scratch/7505708.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 19:33:50] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 19:40:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 20:02:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 20:27:11] Resuming TopHat pipeline with unmapped reads
[2019-07-03 20:27:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 21:34:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 21:45:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 21:57:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:10:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:22:12] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:29:45] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:33:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 23:40:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 23:53:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 00:06:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 00:20:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 00:33:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 00:42:30] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 00:46:57] Searching for junctions via segment mapping
[2019-07-04 13:39:52] Retrieving sequences for splices
[2019-07-04 13:42:20] Indexing splices
[2019-07-04 13:43:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 13:56:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 14:09:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 14:23:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 14:36:41] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 14:44:13] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 14:45:53] Joining segment hits
[2019-07-04 15:06:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 15:19:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 15:33:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 15:46:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 15:59:04] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 16:06:17] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 16:08:02] Joining segment hits
[2019-07-04 16:28:51] Reporting output tracks
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[2019-07-04 17:48:15] A summary of the alignment counts can be found in /scratch/7505708.1.linga/tophat2/align_summary.txt
[2019-07-04 17:48:15] Run complete: 22:48:26 elapsed