[2018-10-13 02:02:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:02:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:02:50] Checking for Bowtie index files (genome)..
[2018-10-13 02:02:50] Checking for reference FASTA file
[2018-10-13 02:02:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:02:52] Reading known junctions from GTF file
[2018-10-13 02:02:54] Preparing reads
	 left reads: min. length=100, max. length=100, 497174 kept reads (256 discarded)
	right reads: min. length=100, max. length=100, 496770 kept reads (660 discarded)
[2018-10-13 02:03:09] Building transcriptome data files /scratch/8792905.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:03:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:08:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:08:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:08:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:08:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:09:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:09:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:09:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:09:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:09:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:10:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:10:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:10:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:10:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:10:27] Searching for junctions via segment mapping
[2018-10-13 02:11:52] Retrieving sequences for splices
[2018-10-13 02:12:59] Indexing splices
[2018-10-13 02:13:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:13:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:13:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:13:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:13:19] Joining segment hits
[2018-10-13 02:14:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:14:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:14:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:14:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:14:44] Joining segment hits
[2018-10-13 02:15:59] Reporting output tracks
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[2018-10-13 02:18:00] A summary of the alignment counts can be found in /scratch/8792905.1.p8/tophat2/align_summary.txt
[2018-10-13 02:18:00] Run complete: 00:15:10 elapsed