[2018-10-13 09:02:01] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:02:01] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:02:02] Checking for Bowtie index files (genome)..
[2018-10-13 09:02:02] Checking for reference FASTA file
[2018-10-13 09:02:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:02:03] Reading known junctions from GTF file
[2018-10-13 09:02:06] Preparing reads
	 left reads: min. length=100, max. length=100, 856367 kept reads (154 discarded)
	right reads: min. length=100, max. length=100, 856165 kept reads (356 discarded)
[2018-10-13 09:02:30] Building transcriptome data files /scratch/8793133.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:02:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:07:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:08:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:08:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:08:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:08:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:09:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:09:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:09:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:09:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:09:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:09:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:09:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:09:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:10:00] Searching for junctions via segment mapping
[2018-10-13 09:12:35] Retrieving sequences for splices
[2018-10-13 09:13:42] Indexing splices
[2018-10-13 09:13:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:13:58] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:14:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:14:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:14:09] Joining segment hits
[2018-10-13 09:15:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:15:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:15:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:15:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:15:39] Joining segment hits
[2018-10-13 09:16:55] Reporting output tracks
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[2018-10-13 09:24:37] A summary of the alignment counts can be found in /scratch/8793133.1.p16/tophat2/align_summary.txt
[2018-10-13 09:24:37] Run complete: 00:22:35 elapsed