[2018-10-13 15:03:13] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:03:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:03:13] Checking for Bowtie index files (genome)..
[2018-10-13 15:03:13] Checking for reference FASTA file
[2018-10-13 15:03:13] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:03:15] Reading known junctions from GTF file
[2018-10-13 15:03:18] Preparing reads
	 left reads: min. length=100, max. length=100, 752556 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 752291 kept reads (389 discarded)
[2018-10-13 15:03:37] Building transcriptome data files /scratch/8793308.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:03:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:08:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:08:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:09:28] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:09:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:09:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:09:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:09:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:10:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:10:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:10:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:10:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:10:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:10:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:10:46] Searching for junctions via segment mapping
[2018-10-13 15:12:58] Retrieving sequences for splices
[2018-10-13 15:14:04] Indexing splices
[2018-10-13 15:14:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:14:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:14:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:14:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:14:27] Joining segment hits
[2018-10-13 15:15:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:15:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:15:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:15:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:15:54] Joining segment hits
[2018-10-13 15:17:10] Reporting output tracks
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[2018-10-13 15:21:42] A summary of the alignment counts can be found in /scratch/8793308.1.p16/tophat2/align_summary.txt
[2018-10-13 15:21:42] Run complete: 00:18:28 elapsed