[2019-07-12 13:46:11] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:46:11] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:46:11] Checking for Bowtie index files (genome)..
[2019-07-12 13:46:11] Checking for reference FASTA file
[2019-07-12 13:46:11] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:46:14] Reading known junctions from GTF file
[2019-07-12 13:46:17] Preparing reads
	 left reads: min. length=151, max. length=151, 51667322 kept reads (87 discarded)
	right reads: min. length=151, max. length=151, 51661796 kept reads (5613 discarded)
[2019-07-12 14:47:29] Building transcriptome data files /scratch/7678192.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:47:47] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:54:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:28:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:08:58] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:08:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 18:02:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 18:20:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 18:40:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 19:00:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 19:19:05] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 19:34:02] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 19:45:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 22:01:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 22:22:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 22:44:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 23:06:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 23:26:49] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 23:44:46] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 23:59:21] Searching for junctions via segment mapping
[2019-07-13 08:37:26] Retrieving sequences for splices
[2019-07-13 08:39:54] Indexing splices
[2019-07-13 08:41:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 08:57:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 09:15:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 09:31:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 09:46:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 09:59:34] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 10:06:34] Joining segment hits
[2019-07-13 10:40:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 11:00:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 11:20:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 11:39:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 11:57:05] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 12:10:16] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 12:17:52] Joining segment hits
[2019-07-13 12:50:11] Reporting output tracks
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[2019-07-13 15:04:39] A summary of the alignment counts can be found in /scratch/7678192.1.linga/tophat2/align_summary.txt
[2019-07-13 15:04:39] Run complete: 1 days 01:18:28 elapsed