[2018-10-12 23:56:19] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:56:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:56:19] Checking for Bowtie index files (genome)..
[2018-10-12 23:56:19] Checking for reference FASTA file
[2018-10-12 23:56:19] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:56:21] Reading known junctions from GTF file
[2018-10-12 23:56:23] Preparing reads
	 left reads: min. length=100, max. length=100, 267397 kept reads (181 discarded)
	right reads: min. length=100, max. length=100, 267085 kept reads (493 discarded)
[2018-10-12 23:56:31] Building transcriptome data files /scratch/8792851.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:56:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:01:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:01:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:02:00] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:02:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:02:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:02:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:02:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:02:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:02:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:02:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:03:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:03:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:03:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:03:14] Searching for junctions via segment mapping
[2018-10-13 00:04:30] Retrieving sequences for splices
[2018-10-13 00:05:36] Indexing splices
[2018-10-13 00:05:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:05:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:05:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:05:55] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:05:58] Joining segment hits
[2018-10-13 00:07:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:07:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:07:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:07:14] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:07:16] Joining segment hits
[2018-10-13 00:08:25] Reporting output tracks
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[2018-10-13 00:09:59] A summary of the alignment counts can be found in /scratch/8792851.1.p8/tophat2/align_summary.txt
[2018-10-13 00:09:59] Run complete: 00:13:39 elapsed