[2018-10-13 16:24:47] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:24:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:24:47] Checking for Bowtie index files (genome)..
[2018-10-13 16:24:47] Checking for reference FASTA file
[2018-10-13 16:24:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:24:49] Reading known junctions from GTF file
[2018-10-13 16:24:51] Preparing reads
	 left reads: min. length=100, max. length=100, 419548 kept reads (288 discarded)
	right reads: min. length=100, max. length=100, 419281 kept reads (555 discarded)
[2018-10-13 16:25:04] Building transcriptome data files /scratch/8793353.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:25:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:30:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:30:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:30:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:30:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:30:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:31:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:31:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:31:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:31:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:31:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:31:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:31:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:31:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:31:51] Searching for junctions via segment mapping
[2018-10-13 16:33:29] Retrieving sequences for splices
[2018-10-13 16:34:36] Indexing splices
[2018-10-13 16:34:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:34:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:34:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:34:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:34:57] Joining segment hits
[2018-10-13 16:36:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:36:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:36:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:36:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:36:20] Joining segment hits
[2018-10-13 16:37:34] Reporting output tracks
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[2018-10-13 16:39:56] A summary of the alignment counts can be found in /scratch/8793353.1.p8/tophat2/align_summary.txt
[2018-10-13 16:39:56] Run complete: 00:15:09 elapsed