[2018-10-13 17:04:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:04:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:04:50] Checking for Bowtie index files (genome)..
[2018-10-13 17:04:50] Checking for reference FASTA file
[2018-10-13 17:04:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:04:52] Reading known junctions from GTF file
[2018-10-13 17:04:54] Preparing reads
	 left reads: min. length=100, max. length=100, 225940 kept reads (274 discarded)
	right reads: min. length=100, max. length=100, 225723 kept reads (491 discarded)
[2018-10-13 17:05:01] Building transcriptome data files /scratch/8793386.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:05:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:09:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:10:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:10:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:10:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:10:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:10:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:10:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:10:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:10:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:11:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:11:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:11:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:11:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:11:17] Searching for junctions via segment mapping
[2018-10-13 17:12:31] Retrieving sequences for splices
[2018-10-13 17:13:37] Indexing splices
[2018-10-13 17:13:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:13:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:13:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:13:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:13:57] Joining segment hits
[2018-10-13 17:15:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:15:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:15:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:15:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:15:13] Joining segment hits
[2018-10-13 17:16:23] Reporting output tracks
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[2018-10-13 17:17:47] A summary of the alignment counts can be found in /scratch/8793386.1.p16/tophat2/align_summary.txt
[2018-10-13 17:17:47] Run complete: 00:12:57 elapsed