[2019-07-12 22:10:15] Beginning TopHat run (v2.1.1)
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[2019-07-12 22:10:15] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 22:10:18] Checking for Bowtie index files (genome)..
[2019-07-12 22:10:18] Checking for reference FASTA file
[2019-07-12 22:10:18] Generating SAM header for Bowtie2Index/genome
[2019-07-12 22:10:34] Reading known junctions from GTF file
[2019-07-12 22:10:39] Preparing reads
	 left reads: min. length=150, max. length=150, 70942364 kept reads (6384 discarded)
	right reads: min. length=150, max. length=150, 70931422 kept reads (17326 discarded)
[2019-07-13 00:26:02] Building transcriptome data files /scratch/7682057.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-13 00:26:44] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-13 00:39:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 01:58:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-13 03:21:29] Resuming TopHat pipeline with unmapped reads
[2019-07-13 03:21:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 07:24:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 07:55:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 08:31:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 09:07:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 09:42:00] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 10:08:22] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 10:19:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 14:31:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 15:09:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 15:47:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 16:28:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 17:06:05] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 17:35:58] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 17:54:32] Searching for junctions via segment mapping
[2019-07-14 15:22:57] Retrieving sequences for splices
[2019-07-14 15:27:08] Indexing splices
[2019-07-14 15:28:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 15:54:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 16:19:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 16:46:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 17:15:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 17:33:39] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 17:37:55] Joining segment hits
[2019-07-14 18:16:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 18:48:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 19:19:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 19:50:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 20:21:13] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 20:41:30] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 20:46:17] Joining segment hits
[2019-07-14 21:34:03] Reporting output tracks
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[2019-07-15 02:00:31] A summary of the alignment counts can be found in /scratch/7682057.1.linga/tophat2/align_summary.txt
[2019-07-15 02:00:31] Run complete: 2 days 03:50:15 elapsed