[2018-10-13 16:41:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:41:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:41:15] Checking for Bowtie index files (genome)..
[2018-10-13 16:41:15] Checking for reference FASTA file
[2018-10-13 16:41:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:41:17] Reading known junctions from GTF file
[2018-10-13 16:41:19] Preparing reads
	 left reads: min. length=100, max. length=100, 146136 kept reads (232 discarded)
	right reads: min. length=100, max. length=100, 145967 kept reads (401 discarded)
[2018-10-13 16:41:23] Building transcriptome data files /scratch/8793367.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:41:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:46:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:46:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:47:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:47:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:47:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:47:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:47:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:47:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:47:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:47:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:47:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:47:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:47:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:47:54] Searching for junctions via segment mapping
[2018-10-13 16:49:07] Retrieving sequences for splices
[2018-10-13 16:50:14] Indexing splices
[2018-10-13 16:50:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:50:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:50:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:50:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:50:32] Joining segment hits
[2018-10-13 16:51:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:51:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:51:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:51:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:51:49] Joining segment hits
[2018-10-13 16:52:57] Reporting output tracks
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[2018-10-13 16:54:14] A summary of the alignment counts can be found in /scratch/8793367.1.p8/tophat2/align_summary.txt
[2018-10-13 16:54:14] Run complete: 00:12:59 elapsed