[2018-10-13 18:01:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:01:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:01:34] Checking for Bowtie index files (genome)..
[2018-10-13 18:01:34] Checking for reference FASTA file
[2018-10-13 18:01:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:01:36] Reading known junctions from GTF file
[2018-10-13 18:01:38] Preparing reads
	 left reads: min. length=100, max. length=100, 705668 kept reads (372 discarded)
	right reads: min. length=100, max. length=100, 705309 kept reads (731 discarded)
[2018-10-13 18:01:59] Building transcriptome data files /scratch/8793423.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:02:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:06:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:07:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:07:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:07:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:08:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:08:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:08:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:08:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:08:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:09:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:09:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:09:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:09:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:09:39] Searching for junctions via segment mapping
[2018-10-13 18:11:10] Retrieving sequences for splices
[2018-10-13 18:12:17] Indexing splices
[2018-10-13 18:12:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:12:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:12:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:12:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:12:38] Joining segment hits
[2018-10-13 18:13:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:13:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:13:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:14:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:14:03] Joining segment hits
[2018-10-13 18:15:19] Reporting output tracks
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[2018-10-13 18:17:35] A summary of the alignment counts can be found in /scratch/8793423.1.p8/tophat2/align_summary.txt
[2018-10-13 18:17:35] Run complete: 00:16:01 elapsed