[2018-10-13 06:23:45] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:23:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:23:45] Checking for Bowtie index files (genome)..
[2018-10-13 06:23:45] Checking for reference FASTA file
[2018-10-13 06:23:45] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:23:47] Reading known junctions from GTF file
[2018-10-13 06:23:49] Preparing reads
	 left reads: min. length=100, max. length=100, 911657 kept reads (71 discarded)
	right reads: min. length=100, max. length=100, 911488 kept reads (240 discarded)
[2018-10-13 06:24:17] Building transcriptome data files /scratch/8793054.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:24:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:29:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:29:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:30:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:30:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:30:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:30:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:30:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:30:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:30:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:31:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:31:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:31:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:31:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:31:38] Searching for junctions via segment mapping
[2018-10-13 06:34:03] Retrieving sequences for splices
[2018-10-13 06:35:11] Indexing splices
[2018-10-13 06:35:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:35:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:35:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:35:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:35:34] Joining segment hits
[2018-10-13 06:36:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:36:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:36:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:37:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:37:03] Joining segment hits
[2018-10-13 06:38:19] Reporting output tracks
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[2018-10-13 06:45:01] A summary of the alignment counts can be found in /scratch/8793054.1.p16/tophat2/align_summary.txt
[2018-10-13 06:45:01] Run complete: 00:21:16 elapsed