[2019-07-12 13:47:21] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:47:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:47:22] Checking for Bowtie index files (genome)..
[2019-07-12 13:47:22] Checking for reference FASTA file
[2019-07-12 13:47:22] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:47:24] Reading known junctions from GTF file
[2019-07-12 13:47:27] Preparing reads
	 left reads: min. length=151, max. length=151, 65907136 kept reads (4410 discarded)
	right reads: min. length=151, max. length=151, 65896535 kept reads (15011 discarded)
[2019-07-12 15:00:14] Building transcriptome data files /scratch/7678195.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:00:30] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:06:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:51:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:43:29] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:43:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:57:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 20:33:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 21:10:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:48:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 22:25:03] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:55:51] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 23:18:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:12:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:54:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:38:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:24:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 05:06:29] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:42:56] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 06:12:09] Searching for junctions via segment mapping
[2019-07-13 14:36:26] Retrieving sequences for splices
[2019-07-13 14:38:55] Indexing splices
[2019-07-13 14:40:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 15:12:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 15:43:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 16:13:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 16:44:58] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 17:06:48] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 17:19:13] Joining segment hits
[2019-07-13 18:10:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 18:43:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 19:15:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 19:47:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 20:18:26] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 20:45:36] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 21:03:08] Joining segment hits
[2019-07-13 21:59:27] Reporting output tracks
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[2019-07-13 23:55:17] A summary of the alignment counts can be found in /scratch/7678195.1.linga/tophat2/align_summary.txt
[2019-07-13 23:55:17] Run complete: 1 days 10:07:56 elapsed