[2019-07-17 19:14:24] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:14:24] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:26] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:26] Checking for reference FASTA file
[2019-07-17 19:14:26] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:32] Reading known junctions from GTF file
[2019-07-17 19:14:36] Preparing reads
	 left reads: min. length=150, max. length=150, 70942364 kept reads (6384 discarded)
	right reads: min. length=150, max. length=150, 70931422 kept reads (17326 discarded)
[2019-07-17 20:26:23] Building transcriptome data files /scratch/7775061.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:26:49] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:35:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:39:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:46:17] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:46:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:55:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 01:14:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 01:36:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 01:56:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 02:15:42] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 02:29:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 02:35:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 04:56:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 05:19:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 05:41:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 06:05:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 06:27:20] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 06:43:57] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 06:53:17] Searching for junctions via segment mapping
[2019-07-19 02:58:36] Retrieving sequences for splices
[2019-07-19 03:00:44] Indexing splices
[2019-07-19 03:02:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 03:18:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 03:35:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 03:52:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 04:09:15] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 04:21:06] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 04:24:16] Joining segment hits
[2019-07-19 04:52:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-19 05:11:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-19 05:29:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-19 05:47:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-19 06:04:18] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-19 06:15:30] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-19 06:18:08] Joining segment hits
[2019-07-19 06:44:33] Reporting output tracks
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[2019-07-19 09:01:06] A summary of the alignment counts can be found in /scratch/7775061.1.linga/tophat2/align_summary.txt
[2019-07-19 09:01:06] Run complete: 1 days 13:46:42 elapsed