[2018-10-13 18:38:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:38:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:38:53] Checking for Bowtie index files (genome)..
[2018-10-13 18:38:53] Checking for reference FASTA file
[2018-10-13 18:38:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:38:55] Reading known junctions from GTF file
[2018-10-13 18:38:57] Preparing reads
	 left reads: min. length=100, max. length=100, 419866 kept reads (258 discarded)
	right reads: min. length=100, max. length=100, 419599 kept reads (525 discarded)
[2018-10-13 18:39:09] Building transcriptome data files /scratch/8793449.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:39:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:44:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:44:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:45:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:45:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:45:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:45:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:45:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:45:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:45:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:46:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:46:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:46:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:32] Searching for junctions via segment mapping
[2018-10-13 18:47:54] Retrieving sequences for splices
[2018-10-13 18:49:01] Indexing splices
[2018-10-13 18:49:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:49:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:49:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:49:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:49:21] Joining segment hits
[2018-10-13 18:50:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:50:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:50:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:50:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:50:45] Joining segment hits
[2018-10-13 18:51:59] Reporting output tracks
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[2018-10-13 18:53:46] A summary of the alignment counts can be found in /scratch/8793449.1.p8/tophat2/align_summary.txt
[2018-10-13 18:53:46] Run complete: 00:14:53 elapsed