[2018-10-13 15:06:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:06:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:06:21] Checking for Bowtie index files (genome)..
[2018-10-13 15:06:21] Checking for reference FASTA file
[2018-10-13 15:06:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:06:23] Reading known junctions from GTF file
[2018-10-13 15:06:25] Preparing reads
	 left reads: min. length=100, max. length=100, 519278 kept reads (64 discarded)
	right reads: min. length=100, max. length=100, 519100 kept reads (242 discarded)
[2018-10-13 15:06:40] Building transcriptome data files /scratch/8793311.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:06:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:11:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:11:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:12:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:12:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:12:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:12:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:12:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:12:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:12:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:13:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:13:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:13:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:13:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:13:23] Searching for junctions via segment mapping
[2018-10-13 15:15:00] Retrieving sequences for splices
[2018-10-13 15:16:07] Indexing splices
[2018-10-13 15:16:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:16:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:16:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:16:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:16:28] Joining segment hits
[2018-10-13 15:17:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:17:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:17:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:17:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:17:52] Joining segment hits
[2018-10-13 15:19:07] Reporting output tracks
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[2018-10-13 15:21:54] A summary of the alignment counts can be found in /scratch/8793311.1.p16/tophat2/align_summary.txt
[2018-10-13 15:21:54] Run complete: 00:15:33 elapsed