[2018-10-13 17:27:54] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:27:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:27:54] Checking for Bowtie index files (genome)..
[2018-10-13 17:27:54] Checking for reference FASTA file
[2018-10-13 17:27:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:27:56] Reading known junctions from GTF file
[2018-10-13 17:27:59] Preparing reads
	 left reads: min. length=100, max. length=100, 321129 kept reads (243 discarded)
	right reads: min. length=100, max. length=100, 320934 kept reads (438 discarded)
[2018-10-13 17:28:08] Building transcriptome data files /scratch/8793398.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:28:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:33:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:33:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:33:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:33:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:33:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:33:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:34:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:34:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:34:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:34:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:34:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:34:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:34:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:34:44] Searching for junctions via segment mapping
[2018-10-13 17:36:03] Retrieving sequences for splices
[2018-10-13 17:37:10] Indexing splices
[2018-10-13 17:37:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:37:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:37:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:37:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:37:29] Joining segment hits
[2018-10-13 17:38:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:38:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:38:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:38:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:38:47] Joining segment hits
[2018-10-13 17:39:56] Reporting output tracks
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[2018-10-13 17:41:35] A summary of the alignment counts can be found in /scratch/8793398.1.p8/tophat2/align_summary.txt
[2018-10-13 17:41:35] Run complete: 00:13:40 elapsed