[2019-07-17 19:14:33] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:14:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:36] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:38] Checking for reference FASTA file
[2019-07-17 19:14:38] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:43] Reading known junctions from GTF file
[2019-07-17 19:14:46] Preparing reads
	 left reads: min. length=150, max. length=150, 80976020 kept reads (7383 discarded)
	right reads: min. length=150, max. length=150, 80963148 kept reads (20255 discarded)
[2019-07-17 20:40:01] Building transcriptome data files /scratch/7775064.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:40:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:48:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:50:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:54:59] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:54:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 01:26:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 01:48:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 02:10:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 02:29:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 02:48:47] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 03:02:46] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 03:10:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 06:14:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 06:38:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 07:05:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 07:32:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 07:57:02] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 08:16:07] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 08:28:31] Searching for junctions via segment mapping
[2019-07-19 00:15:56] Retrieving sequences for splices
[2019-07-19 00:18:20] Indexing splices
[2019-07-19 00:19:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 00:33:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 00:49:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 01:04:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 01:20:57] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 01:31:34] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 01:34:27] Joining segment hits
[2019-07-19 02:00:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 02:16:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 02:31:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 02:47:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 03:02:20] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 03:12:18] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 03:15:11] Joining segment hits
[2019-07-19 03:41:15] Reporting output tracks
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[2019-07-19 05:54:06] A summary of the alignment counts can be found in /scratch/7775064.1.linga/tophat2/align_summary.txt
[2019-07-19 05:54:06] Run complete: 1 days 10:39:33 elapsed