[2019-07-18 10:32:13] Beginning TopHat run (v2.1.1)
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[2019-07-18 10:32:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-18 10:32:14] Checking for Bowtie index files (genome)..
[2019-07-18 10:32:14] Checking for reference FASTA file
[2019-07-18 10:32:14] Generating SAM header for Bowtie2Index/genome
[2019-07-18 10:32:19] Reading known junctions from GTF file
[2019-07-18 10:32:22] Preparing reads
	 left reads: min. length=151, max. length=151, 60170033 kept reads (128 discarded)
	right reads: min. length=151, max. length=151, 60163523 kept reads (6638 discarded)
[2019-07-18 11:40:51] Building transcriptome data files /scratch/7790731.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-18 11:41:10] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-18 11:47:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-18 12:39:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-18 13:32:43] Resuming TopHat pipeline with unmapped reads
[2019-07-18 13:32:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 15:10:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 15:33:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 15:56:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 16:18:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 16:40:01] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 16:56:49] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 17:07:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 18:51:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 19:15:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 19:39:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 20:02:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 20:25:40] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 20:44:09] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 20:57:36] Searching for junctions via segment mapping
[2019-07-19 14:43:53] Retrieving sequences for splices
[2019-07-19 14:46:04] Indexing splices
[2019-07-19 14:48:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 15:08:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 15:28:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 15:49:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 16:08:15] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 16:22:31] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 16:28:04] Joining segment hits
[2019-07-19 17:03:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 17:25:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 17:46:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 18:07:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 18:27:33] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 18:42:02] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 18:48:34] Joining segment hits
[2019-07-19 19:25:17] Reporting output tracks
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[2019-07-19 22:14:39] A summary of the alignment counts can be found in /scratch/7790731.1.linga/tophat2/align_summary.txt
[2019-07-19 22:14:39] Run complete: 1 days 11:42:25 elapsed