[2018-10-13 04:47:33] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:47:33] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:47:33] Checking for Bowtie index files (genome)..
[2018-10-13 04:47:33] Checking for reference FASTA file
[2018-10-13 04:47:33] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:47:35] Reading known junctions from GTF file
[2018-10-13 04:47:37] Preparing reads
	 left reads: min. length=100, max. length=100, 584882 kept reads (180 discarded)
	right reads: min. length=100, max. length=100, 584700 kept reads (362 discarded)
[2018-10-13 04:47:53] Building transcriptome data files /scratch/8793003.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:48:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:52:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:53:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:53:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:53:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:53:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:53:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:54:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:54:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:54:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:54:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:54:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:54:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:54:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:54:55] Searching for junctions via segment mapping
[2018-10-13 04:56:35] Retrieving sequences for splices
[2018-10-13 04:57:42] Indexing splices
[2018-10-13 04:57:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:57:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:57:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:58:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:58:03] Joining segment hits
[2018-10-13 04:59:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:59:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:59:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:59:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:59:29] Joining segment hits
[2018-10-13 05:00:45] Reporting output tracks
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[2018-10-13 05:03:26] A summary of the alignment counts can be found in /scratch/8793003.1.p16/tophat2/align_summary.txt
[2018-10-13 05:03:26] Run complete: 00:15:53 elapsed