[2019-07-12 13:38:26] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:38:26] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:38:26] Checking for Bowtie index files (genome)..
[2019-07-12 13:38:26] Checking for reference FASTA file
[2019-07-12 13:38:26] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:38:33] Reading known junctions from GTF file
[2019-07-12 13:38:37] Preparing reads
	 left reads: min. length=151, max. length=151, 74861571 kept reads (4989 discarded)
	right reads: min. length=151, max. length=151, 74849424 kept reads (17136 discarded)
[2019-07-12 15:16:12] Building transcriptome data files /scratch/7678207.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:16:34] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:24:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:21:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 17:15:29] Resuming TopHat pipeline with unmapped reads
[2019-07-12 17:15:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 20:14:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 21:02:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 21:51:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 22:39:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 23:28:54] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 00:09:00] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 00:38:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 05:26:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 06:17:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 07:06:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 07:52:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 08:38:21] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 09:16:23] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 09:46:17] Searching for junctions via segment mapping
[2019-07-13 12:36:40] Retrieving sequences for splices
[2019-07-13 12:38:43] Indexing splices
[2019-07-13 12:39:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 13:04:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 13:29:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 13:53:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 14:18:53] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 14:39:03] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 14:51:30] Joining segment hits
[2019-07-13 15:38:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 16:04:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 16:30:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 16:56:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 17:22:36] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 17:43:40] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 17:57:42] Joining segment hits
[2019-07-13 18:41:46] Reporting output tracks
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[2019-07-13 20:07:08] A summary of the alignment counts can be found in /scratch/7678207.1.linga/tophat2/align_summary.txt
[2019-07-13 20:07:08] Run complete: 1 days 06:28:42 elapsed