[2018-10-13 01:40:43] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:40:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:40:43] Checking for Bowtie index files (genome)..
[2018-10-13 01:40:43] Checking for reference FASTA file
[2018-10-13 01:40:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:40:45] Reading known junctions from GTF file
[2018-10-13 01:40:48] Preparing reads
	 left reads: min. length=100, max. length=100, 272482 kept reads (196 discarded)
	right reads: min. length=100, max. length=100, 272233 kept reads (445 discarded)
[2018-10-13 01:40:55] Building transcriptome data files /scratch/8792893.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:41:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:45:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:46:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:46:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:46:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:46:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:46:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:46:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:46:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:46:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:47:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:47:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:47:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:47:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:47:36] Searching for junctions via segment mapping
[2018-10-13 01:48:51] Retrieving sequences for splices
[2018-10-13 01:49:57] Indexing splices
[2018-10-13 01:50:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:50:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:50:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:50:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:50:16] Joining segment hits
[2018-10-13 01:51:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:51:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:51:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:51:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:51:34] Joining segment hits
[2018-10-13 01:52:44] Reporting output tracks
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[2018-10-13 01:54:19] A summary of the alignment counts can be found in /scratch/8792893.1.p16/tophat2/align_summary.txt
[2018-10-13 01:54:19] Run complete: 00:13:35 elapsed