[2019-07-03 20:12:00] Beginning TopHat run (v2.1.1)
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[2019-07-03 20:12:00] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 20:12:00] Checking for Bowtie index files (genome)..
[2019-07-03 20:12:00] Checking for reference FASTA file
[2019-07-03 20:12:00] Generating SAM header for Bowtie2Index/genome
[2019-07-03 20:12:03] Reading known junctions from GTF file
[2019-07-03 20:12:07] Preparing reads
	 left reads: min. length=150, max. length=150, 33055508 kept reads (431 discarded)
	right reads: min. length=150, max. length=150, 33055853 kept reads (86 discarded)
[2019-07-03 20:54:17] Building transcriptome data files /scratch/7505710.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 20:54:37] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 21:01:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 21:25:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 21:47:42] Resuming TopHat pipeline with unmapped reads
[2019-07-03 21:47:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 23:14:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 23:26:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 23:38:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 23:50:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 00:03:33] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 00:11:47] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 00:15:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 01:40:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 01:54:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 02:08:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 02:21:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 02:35:01] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 02:44:31] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 02:49:15] Searching for junctions via segment mapping
[2019-07-04 11:27:05] Retrieving sequences for splices
[2019-07-04 11:29:51] Indexing splices
[2019-07-04 11:30:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 11:39:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 11:48:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 11:57:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 12:06:45] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 12:12:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 12:13:43] Joining segment hits
[2019-07-04 12:34:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 12:48:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 13:01:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 13:13:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 13:23:52] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 13:29:15] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 13:30:42] Joining segment hits
[2019-07-04 13:48:13] Reporting output tracks
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[2019-07-04 14:58:29] A summary of the alignment counts can be found in /scratch/7505710.1.linga/tophat2/align_summary.txt
[2019-07-04 14:58:29] Run complete: 18:46:29 elapsed