[2019-07-04 02:21:38] Beginning TopHat run (v2.1.1)
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[2019-07-04 02:21:38] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-04 02:21:38] Checking for Bowtie index files (genome)..
[2019-07-04 02:21:38] Checking for reference FASTA file
[2019-07-04 02:21:38] Generating SAM header for Bowtie2Index/genome
[2019-07-04 02:21:40] Reading known junctions from GTF file
[2019-07-04 02:21:44] Preparing reads
	 left reads: min. length=150, max. length=150, 31878539 kept reads (413 discarded)
	right reads: min. length=150, max. length=150, 31878882 kept reads (70 discarded)
[2019-07-04 02:52:55] Building transcriptome data files /scratch/7505713.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 02:53:10] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 02:59:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:15:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:31:59] Resuming TopHat pipeline with unmapped reads
[2019-07-04 03:31:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 04:24:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 04:32:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 04:40:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 04:48:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 04:56:44] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 05:02:13] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 05:05:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 06:04:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 06:13:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 06:22:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 06:31:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 06:40:43] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 06:47:18] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 06:51:06] Searching for junctions via segment mapping
[2019-07-04 10:04:17] Retrieving sequences for splices
[2019-07-04 10:06:37] Indexing splices
[2019-07-04 10:07:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 10:13:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 10:18:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 10:24:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 10:30:43] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 10:34:18] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 10:35:18] Joining segment hits
[2019-07-04 10:47:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 10:53:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 10:59:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 11:05:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 11:11:10] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 11:14:45] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 11:15:51] Joining segment hits
[2019-07-04 11:27:53] Reporting output tracks
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[2019-07-04 12:16:57] A summary of the alignment counts can be found in /scratch/7505713.1.linga/tophat2/align_summary.txt
[2019-07-04 12:16:57] Run complete: 09:55:19 elapsed