[2018-10-12 21:05:18] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:05:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:05:19] Checking for Bowtie index files (genome)..
[2018-10-12 21:05:19] Checking for reference FASTA file
[2018-10-12 21:05:19] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:05:20] Reading known junctions from GTF file
[2018-10-12 21:05:23] Preparing reads
	 left reads: min. length=100, max. length=100, 252846 kept reads (190 discarded)
	right reads: min. length=100, max. length=100, 252664 kept reads (372 discarded)
[2018-10-12 21:05:30] Building transcriptome data files /scratch/8792744.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:05:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:10:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:10:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:10:50] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:10:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:11:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:11:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:11:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:11:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:11:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:11:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:11:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:11:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:11:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:11:52] Searching for junctions via segment mapping
[2018-10-12 21:13:08] Retrieving sequences for splices
[2018-10-12 21:14:15] Indexing splices
[2018-10-12 21:14:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:14:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:14:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:14:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:14:34] Joining segment hits
[2018-10-12 21:15:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:15:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:15:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:15:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:15:52] Joining segment hits
[2018-10-12 21:17:01] Reporting output tracks
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[2018-10-12 21:18:30] A summary of the alignment counts can be found in /scratch/8792744.1.p16/tophat2/align_summary.txt
[2018-10-12 21:18:30] Run complete: 00:13:11 elapsed