[2018-10-12 22:13:53] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:13:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:13:53] Checking for Bowtie index files (genome)..
[2018-10-12 22:13:53] Checking for reference FASTA file
[2018-10-12 22:13:53] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:13:55] Reading known junctions from GTF file
[2018-10-12 22:13:57] Preparing reads
	 left reads: min. length=100, max. length=100, 200528 kept reads (239 discarded)
	right reads: min. length=100, max. length=100, 200410 kept reads (357 discarded)
[2018-10-12 22:14:02] Building transcriptome data files /scratch/8792787.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:14:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:18:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:19:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:19:23] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:19:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:19:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:19:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:19:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:19:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:19:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:20:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:20:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:20:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:20:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:20:34] Searching for junctions via segment mapping
[2018-10-12 22:21:47] Retrieving sequences for splices
[2018-10-12 22:22:54] Indexing splices
[2018-10-12 22:23:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:23:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:23:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:23:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:23:13] Joining segment hits
[2018-10-12 22:24:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:24:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:24:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:24:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:24:31] Joining segment hits
[2018-10-12 22:25:40] Reporting output tracks
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[2018-10-12 22:27:14] A summary of the alignment counts can be found in /scratch/8792787.1.p8/tophat2/align_summary.txt
[2018-10-12 22:27:14] Run complete: 00:13:21 elapsed