[2018-10-12 22:12:59] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:12:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:12:59] Checking for Bowtie index files (genome)..
[2018-10-12 22:12:59] Checking for reference FASTA file
[2018-10-12 22:12:59] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:13:01] Reading known junctions from GTF file
[2018-10-12 22:13:04] Preparing reads
	 left reads: min. length=100, max. length=100, 460418 kept reads (256 discarded)
	right reads: min. length=100, max. length=100, 459991 kept reads (683 discarded)
[2018-10-12 22:13:17] Building transcriptome data files /scratch/8792788.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:13:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:18:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:18:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:18:58] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:18:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:19:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:19:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:19:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:19:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:19:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:20:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:20:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:20:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:20:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:20:23] Searching for junctions via segment mapping
[2018-10-12 22:21:56] Retrieving sequences for splices
[2018-10-12 22:23:03] Indexing splices
[2018-10-12 22:23:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:23:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:23:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:23:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:23:23] Joining segment hits
[2018-10-12 22:24:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:24:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:24:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:24:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:24:49] Joining segment hits
[2018-10-12 22:26:04] Reporting output tracks
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[2018-10-12 22:28:15] A summary of the alignment counts can be found in /scratch/8792788.1.p16/tophat2/align_summary.txt
[2018-10-12 22:28:15] Run complete: 00:15:15 elapsed