[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, 56056502 kept reads (113 discarded)
	right reads: min. length=151, max. length=151, 56050707 kept reads (5908 discarded)
[2019-07-12 15:00:17] Building transcriptome data files /scratch/7678202.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:00:34] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:06:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:41:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:34:58] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:34:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:41:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 20:14:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:48:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:23:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:56:04] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:22:24] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:43:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:19:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 03:04:05] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:45:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:21:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:53:32] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:19:03] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:41:38] Searching for junctions via segment mapping
[2019-07-13 07:34:55] Retrieving sequences for splices
[2019-07-13 07:37:26] Indexing splices
[2019-07-13 07:38:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 08:30:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 09:24:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 10:17:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 11:07:38] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 11:46:57] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 12:07:57] Joining segment hits
[2019-07-13 13:15:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 14:05:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 14:56:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 15:48:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 16:38:35] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 17:15:36] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 17:39:57] Joining segment hits
[2019-07-13 18:52:45] Reporting output tracks
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[2019-07-13 20:19:15] A summary of the alignment counts can be found in /scratch/7678202.1.linga/tophat2/align_summary.txt
[2019-07-13 20:19:15] Run complete: 1 days 06:27:01 elapsed