[2018-10-13 02:02:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:02:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:02:51] Checking for Bowtie index files (genome)..
[2018-10-13 02:02:51] Checking for reference FASTA file
[2018-10-13 02:02:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:02:53] Reading known junctions from GTF file
[2018-10-13 02:02:55] Preparing reads
	 left reads: min. length=100, max. length=100, 360991 kept reads (200 discarded)
	right reads: min. length=100, max. length=100, 360625 kept reads (566 discarded)
[2018-10-13 02:03:06] Building transcriptome data files /scratch/8792906.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:03:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:07:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:08:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:08:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:08:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:09:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:09:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:09:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:09:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:09:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:09:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:09:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:09:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:09:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:10:00] Searching for junctions via segment mapping
[2018-10-13 02:11:19] Retrieving sequences for splices
[2018-10-13 02:12:26] Indexing splices
[2018-10-13 02:12:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:12:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:12:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:12:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:12:45] Joining segment hits
[2018-10-13 02:14:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:14:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:14:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:14:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:14:09] Joining segment hits
[2018-10-13 02:15:25] Reporting output tracks
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[2018-10-13 02:17:08] A summary of the alignment counts can be found in /scratch/8792906.1.p16/tophat2/align_summary.txt
[2018-10-13 02:17:08] Run complete: 00:14:16 elapsed