[2019-07-12 13:36:52] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:36:52] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:36:52] Checking for Bowtie index files (genome)..
[2019-07-12 13:36:52] Checking for reference FASTA file
[2019-07-12 13:36:52] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:36:54] Reading known junctions from GTF file
[2019-07-12 13:36:56] Preparing reads
	 left reads: min. length=151, max. length=151, 58692831 kept reads (4019 discarded)
	right reads: min. length=151, max. length=151, 58683248 kept reads (13602 discarded)
[2019-07-12 14:19:14] Building transcriptome data files /scratch/7678210.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:19:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:23:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:02:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:46:36] Resuming TopHat pipeline with unmapped reads
[2019-07-12 15:46:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 17:03:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 17:15:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 17:27:24] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 17:39:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 17:52:22] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 18:03:05] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 18:12:47] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:34:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:47:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:01:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 20:15:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 20:28:53] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 20:40:34] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 20:51:18] Searching for junctions via segment mapping
[2019-07-12 21:30:01] Retrieving sequences for splices
[2019-07-12 21:31:15] Indexing splices
[2019-07-12 21:31:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 21:36:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 21:41:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 21:47:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 21:52:15] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 21:56:42] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 22:00:13] Joining segment hits
[2019-07-12 22:09:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 22:15:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 22:21:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 22:26:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 22:32:39] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 22:37:16] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 22:40:50] Joining segment hits
[2019-07-12 22:50:51] Reporting output tracks
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[2019-07-12 23:40:03] A summary of the alignment counts can be found in /scratch/7678210.1.c/tophat2/align_summary.txt
[2019-07-12 23:40:03] Run complete: 10:03:10 elapsed