[2018-10-13 00:13:13] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:13:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:13:13] Checking for Bowtie index files (genome)..
[2018-10-13 00:13:13] Checking for reference FASTA file
[2018-10-13 00:13:13] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:13:15] Reading known junctions from GTF file
[2018-10-13 00:13:17] Preparing reads
	 left reads: min. length=100, max. length=100, 390737 kept reads (240 discarded)
	right reads: min. length=100, max. length=100, 390314 kept reads (663 discarded)
[2018-10-13 00:13:29] Building transcriptome data files /scratch/8792859.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:13:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:18:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:18:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:19:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:19:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:19:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:19:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:19:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:19:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:20:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:20:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:20:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:20:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:20:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:20:59] Searching for junctions via segment mapping
[2018-10-13 00:22:19] Retrieving sequences for splices
[2018-10-13 00:23:28] Indexing splices
[2018-10-13 00:23:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:23:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:23:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:23:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:23:47] Joining segment hits
[2018-10-13 00:24:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:25:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:25:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:25:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:25:07] Joining segment hits
[2018-10-13 00:26:18] Reporting output tracks
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[2018-10-13 00:28:01] A summary of the alignment counts can be found in /scratch/8792859.1.p8/tophat2/align_summary.txt
[2018-10-13 00:28:01] Run complete: 00:14:48 elapsed