[2018-10-13 13:14:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:14:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:14:31] Checking for Bowtie index files (genome)..
[2018-10-13 13:14:31] Checking for reference FASTA file
[2018-10-13 13:14:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:14:33] Reading known junctions from GTF file
[2018-10-13 13:14:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1268580 kept reads (89 discarded)
	right reads: min. length=100, max. length=100, 1268172 kept reads (497 discarded)
[2018-10-13 13:15:12] Building transcriptome data files /scratch/8793256.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:15:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:20:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:20:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:21:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:21:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:21:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:21:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:21:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:22:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:22:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:22:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:22:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:23:03] Searching for junctions via segment mapping
[2018-10-13 13:25:05] Retrieving sequences for splices
[2018-10-13 13:26:11] Indexing splices
[2018-10-13 13:26:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:26:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:26:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:26:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:26:34] Joining segment hits
[2018-10-13 13:27:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:27:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:27:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:28:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:28:03] Joining segment hits
[2018-10-13 13:29:20] Reporting output tracks
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[2018-10-13 13:34:49] A summary of the alignment counts can be found in /scratch/8793256.1.p16/tophat2/align_summary.txt
[2018-10-13 13:34:49] Run complete: 00:20:18 elapsed