[2018-10-12 22:06:44] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:06:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:06:44] Checking for Bowtie index files (genome)..
[2018-10-12 22:06:44] Checking for reference FASTA file
[2018-10-12 22:06:44] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:06:46] Reading known junctions from GTF file
[2018-10-12 22:06:49] Preparing reads
	 left reads: min. length=100, max. length=100, 620584 kept reads (432 discarded)
	right reads: min. length=100, max. length=100, 620087 kept reads (929 discarded)
[2018-10-12 22:07:06] Building transcriptome data files /scratch/8792783.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:07:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:11:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:13:09] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:13:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:13:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:13:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:13:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:14:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:14:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:14:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:14:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:14:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:06] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:12] Searching for junctions via segment mapping
[2018-10-12 22:16:41] Retrieving sequences for splices
[2018-10-12 22:17:48] Indexing splices
[2018-10-12 22:17:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:18:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:18:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:18:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:18:08] Joining segment hits
[2018-10-12 22:19:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:19:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:19:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:19:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:19:35] Joining segment hits
[2018-10-12 22:20:53] Reporting output tracks
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[2018-10-12 22:23:12] A summary of the alignment counts can be found in /scratch/8792783.1.p16/tophat2/align_summary.txt
[2018-10-12 22:23:12] Run complete: 00:16:27 elapsed