[2018-10-13 13:53:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:53:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:53:51] Checking for Bowtie index files (genome)..
[2018-10-13 13:53:51] Checking for reference FASTA file
[2018-10-13 13:53:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:53:53] Reading known junctions from GTF file
[2018-10-13 13:53:55] Preparing reads
	 left reads: min. length=100, max. length=100, 750258 kept reads (450 discarded)
	right reads: min. length=100, max. length=100, 750049 kept reads (659 discarded)
[2018-10-13 13:54:16] Building transcriptome data files /scratch/8793276.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:54:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:59:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:59:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:00:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:00:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:00:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:00:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:00:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:00:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:01:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:01:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:01:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:01:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:01:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:01:49] Searching for junctions via segment mapping
[2018-10-13 14:03:50] Retrieving sequences for splices
[2018-10-13 14:04:57] Indexing splices
[2018-10-13 14:05:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:05:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:05:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:05:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:05:19] Joining segment hits
[2018-10-13 14:06:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:06:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:06:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:06:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:06:45] Joining segment hits
[2018-10-13 14:08:01] Reporting output tracks
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[2018-10-13 14:12:02] A summary of the alignment counts can be found in /scratch/8793276.1.p8/tophat2/align_summary.txt
[2018-10-13 14:12:02] Run complete: 00:18:10 elapsed