[2018-10-12 23:34:45] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:34:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:34:45] Checking for Bowtie index files (genome)..
[2018-10-12 23:34:45] Checking for reference FASTA file
[2018-10-12 23:34:45] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:34:47] Reading known junctions from GTF file
[2018-10-12 23:34:49] Preparing reads
	 left reads: min. length=100, max. length=100, 2698710 kept reads (1047 discarded)
	right reads: min. length=100, max. length=100, 2698177 kept reads (1580 discarded)
[2018-10-12 23:35:57] Building transcriptome data files /scratch/8792843.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:36:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:40:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:43:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:45:35] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:45:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:46:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:46:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:47:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:47:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:47:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:48:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:48:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:49:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:49:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:49:47] Searching for junctions via segment mapping
[2018-10-13 00:00:49] Retrieving sequences for splices
[2018-10-13 00:01:57] Indexing splices
[2018-10-13 00:02:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:02:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:02:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:02:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:02:51] Joining segment hits
[2018-10-13 00:04:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:04:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:04:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:04:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:04:56] Joining segment hits
[2018-10-13 00:06:19] Reporting output tracks
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[2018-10-13 00:39:48] A summary of the alignment counts can be found in /scratch/8792843.1.p16/tophat2/align_summary.txt
[2018-10-13 00:39:48] Run complete: 01:05:02 elapsed