[2019-07-03 18:00:14] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:00:14] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:00:14] Checking for Bowtie index files (genome)..
[2019-07-03 18:00:14] Checking for reference FASTA file
[2019-07-03 18:00:14] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:00:16] Reading known junctions from GTF file
[2019-07-03 18:00:20] Preparing reads
	 left reads: min. length=150, max. length=150, 28975382 kept reads (380 discarded)
	right reads: min. length=150, max. length=150, 28975690 kept reads (72 discarded)
[2019-07-03 18:35:44] Building transcriptome data files /scratch/7505703.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:36:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:43:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:58:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:15:52] Resuming TopHat pipeline with unmapped reads
[2019-07-03 19:15:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:25:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:32:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:40:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:48:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:55:56] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 21:00:55] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 21:03:47] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 22:15:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 22:24:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:33:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:43:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:52:35] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:59:39] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 23:03:42] Searching for junctions via segment mapping
[2019-07-04 02:25:27] Retrieving sequences for splices
[2019-07-04 02:28:02] Indexing splices
[2019-07-04 02:29:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:34:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:40:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:46:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 02:51:16] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 02:54:32] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 02:55:34] Joining segment hits
[2019-07-04 03:08:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 03:14:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 03:20:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 03:26:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 03:31:18] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 03:34:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 03:35:47] Joining segment hits
[2019-07-04 03:49:58] Reporting output tracks
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[2019-07-04 04:41:41] A summary of the alignment counts can be found in /scratch/7505703.1.linga/tophat2/align_summary.txt
[2019-07-04 04:41:41] Run complete: 10:41:26 elapsed