[2018-10-13 12:25:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:25:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:25:04] Checking for Bowtie index files (genome)..
[2018-10-13 12:25:04] Checking for reference FASTA file
[2018-10-13 12:25:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:25:06] Reading known junctions from GTF file
[2018-10-13 12:25:09] Preparing reads
	 left reads: min. length=100, max. length=100, 480037 kept reads (188 discarded)
	right reads: min. length=100, max. length=100, 479925 kept reads (300 discarded)
[2018-10-13 12:25:22] Building transcriptome data files /scratch/8793233.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:25:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:30:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:30:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:31:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:31:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:31:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:31:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:31:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:31:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:31:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:31:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:32:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:32:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:32:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:32:16] Searching for junctions via segment mapping
[2018-10-13 12:34:48] Retrieving sequences for splices
[2018-10-13 12:35:54] Indexing splices
[2018-10-13 12:36:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:36:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:36:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:36:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:36:19] Joining segment hits
[2018-10-13 12:37:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:37:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:37:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:37:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:37:47] Joining segment hits
[2018-10-13 12:39:01] Reporting output tracks
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[2018-10-13 12:45:31] A summary of the alignment counts can be found in /scratch/8793233.1.p16/tophat2/align_summary.txt
[2018-10-13 12:45:31] Run complete: 00:20:26 elapsed