[2018-10-12 22:47:31] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:47:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:47:31] Checking for Bowtie index files (genome)..
[2018-10-12 22:47:31] Checking for reference FASTA file
[2018-10-12 22:47:31] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:47:33] Reading known junctions from GTF file
[2018-10-12 22:47:35] Preparing reads
	 left reads: min. length=100, max. length=100, 218538 kept reads (68 discarded)
	right reads: min. length=100, max. length=100, 218420 kept reads (186 discarded)
[2018-10-12 22:47:43] Building transcriptome data files /scratch/8792811.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:48:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:52:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:53:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:53:14] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:53:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:53:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:53:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:53:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:53:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:53:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:53:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:54:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:54:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:54:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:54:16] Searching for junctions via segment mapping
[2018-10-12 22:55:30] Retrieving sequences for splices
[2018-10-12 22:56:36] Indexing splices
[2018-10-12 22:56:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:56:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:56:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:56:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:56:56] Joining segment hits
[2018-10-12 22:58:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:58:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:58:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:58:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:58:12] Joining segment hits
[2018-10-12 22:59:20] Reporting output tracks
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[2018-10-12 23:00:49] A summary of the alignment counts can be found in /scratch/8792811.1.p16/tophat2/align_summary.txt
[2018-10-12 23:00:49] Run complete: 00:13:18 elapsed