[2018-10-13 18:07:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:07:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:07:42] Checking for Bowtie index files (genome)..
[2018-10-13 18:07:42] Checking for reference FASTA file
[2018-10-13 18:07:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:07:44] Reading known junctions from GTF file
[2018-10-13 18:07:46] Preparing reads
	 left reads: min. length=100, max. length=100, 374411 kept reads (258 discarded)
	right reads: min. length=100, max. length=100, 374055 kept reads (614 discarded)
[2018-10-13 18:07:57] Building transcriptome data files /scratch/8793428.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:08:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:12:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:28] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:13:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:13:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:13:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:13:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:13:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:14:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:14:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:14:26] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:14:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:14:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:14:42] Searching for junctions via segment mapping
[2018-10-13 18:16:02] Retrieving sequences for splices
[2018-10-13 18:17:09] Indexing splices
[2018-10-13 18:17:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:17:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:17:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:17:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:17:30] Joining segment hits
[2018-10-13 18:18:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:18:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:18:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:18:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:18:49] Joining segment hits
[2018-10-13 18:20:05] Reporting output tracks
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[2018-10-13 18:21:44] A summary of the alignment counts can be found in /scratch/8793428.1.p16/tophat2/align_summary.txt
[2018-10-13 18:21:44] Run complete: 00:14:01 elapsed