[2019-09-04 14:45:58] Beginning TopHat run (v2.1.1)
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[2019-09-04 14:45:58] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 14:45:59] Checking for Bowtie index files (genome)..
[2019-09-04 14:45:59] Checking for reference FASTA file
[2019-09-04 14:45:59] Generating SAM header for Bowtie2Index/genome
[2019-09-04 14:46:02] Reading known junctions from GTF file
[2019-09-04 14:46:05] Preparing reads
	 left reads: min. length=150, max. length=150, 31471406 kept reads (12 discarded)
	right reads: min. length=150, max. length=150, 31470271 kept reads (1147 discarded)
[2019-09-04 15:11:32] Building transcriptome data files /scratch/9142572.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 15:11:42] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 15:16:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 15:56:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 16:32:25] Resuming TopHat pipeline with unmapped reads
[2019-09-04 16:32:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 17:09:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 17:14:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 17:20:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 17:26:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 17:32:04] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 17:36:45] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 17:39:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 18:14:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 18:19:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 18:25:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 18:30:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 18:36:30] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 18:41:31] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 18:44:24] Searching for junctions via segment mapping
[2019-09-04 18:52:31] Retrieving sequences for splices
[2019-09-04 18:53:33] Indexing splices
[2019-09-04 18:54:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 18:55:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 18:57:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 18:58:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:00:12] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:01:27] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:02:16] Joining segment hits
[2019-09-04 19:06:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 19:07:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 19:08:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 19:10:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 19:11:23] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 19:12:34] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 19:13:36] Joining segment hits
[2019-09-04 19:17:44] Reporting output tracks
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[2019-09-04 19:44:10] A summary of the alignment counts can be found in /scratch/9142572.1.linga/tophat2/align_summary.txt
[2019-09-04 19:44:10] Run complete: 04:58:11 elapsed