[2019-07-03 18:00:13] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:00:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:00:13] Checking for Bowtie index files (genome)..
[2019-07-03 18:00:13] Checking for reference FASTA file
[2019-07-03 18:00:13] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:00:17] Reading known junctions from GTF file
[2019-07-03 18:00:20] Preparing reads
	 left reads: min. length=150, max. length=150, 29823807 kept reads (376 discarded)
	right reads: min. length=150, max. length=150, 29824115 kept reads (68 discarded)
[2019-07-03 18:38:43] Building transcriptome data files /scratch/7505704.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:39:06] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:46:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:06:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:25:38] Resuming TopHat pipeline with unmapped reads
[2019-07-03 19:25:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:25:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:34:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:43:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:52:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 21:01:09] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 21:07:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:10:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 22:06:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 22:16:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:25:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:35:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:45:40] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:53:04] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:57:08] Searching for junctions via segment mapping
[2019-07-04 01:48:52] Retrieving sequences for splices
[2019-07-04 01:51:24] Indexing splices
[2019-07-04 01:52:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 01:57:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:02:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:08:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 02:13:19] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 02:16:32] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 02:17:33] Joining segment hits
[2019-07-04 02:29:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:35:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:41:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:46:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 02:51:43] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 02:54:57] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 02:56:06] Joining segment hits
[2019-07-04 03:09:27] Reporting output tracks
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[2019-07-04 03:59:33] A summary of the alignment counts can be found in /scratch/7505704.1.linga/tophat2/align_summary.txt
[2019-07-04 03:59:33] Run complete: 09:59:19 elapsed