[2019-07-12 13:52:13] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:52:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:52:13] Checking for Bowtie index files (genome)..
[2019-07-12 13:52:13] Checking for reference FASTA file
[2019-07-12 13:52:13] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:52:19] Reading known junctions from GTF file
[2019-07-12 13:52:22] Preparing reads
	 left reads: min. length=151, max. length=151, 77323323 kept reads (5107 discarded)
	right reads: min. length=151, max. length=151, 77310854 kept reads (17576 discarded)
[2019-07-12 15:31:43] Building transcriptome data files /scratch/7678200.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:32:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:43:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 17:06:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 18:17:00] Resuming TopHat pipeline with unmapped reads
[2019-07-12 18:17:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 22:45:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 23:39:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 00:28:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 01:14:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 02:01:11] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 02:45:05] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 03:21:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 07:52:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 08:40:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 09:29:04] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 10:19:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 11:09:55] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 11:51:28] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 12:24:37] Searching for junctions via segment mapping
[2019-07-13 21:42:40] Retrieving sequences for splices
[2019-07-13 21:45:08] Indexing splices
[2019-07-13 21:46:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 22:15:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 22:43:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 23:10:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 23:41:19] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 00:06:49] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 00:18:52] Joining segment hits
[2019-07-14 01:09:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 01:38:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 02:08:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 02:36:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 03:04:40] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 03:26:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 03:40:13] Joining segment hits
[2019-07-14 04:32:56] Reporting output tracks
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[2019-07-14 06:44:40] A summary of the alignment counts can be found in /scratch/7678200.1.linga/tophat2/align_summary.txt
[2019-07-14 06:44:40] Run complete: 1 days 16:52:27 elapsed