[2018-10-13 09:09:35] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:09:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:09:35] Checking for Bowtie index files (genome)..
[2018-10-13 09:09:35] Checking for reference FASTA file
[2018-10-13 09:09:35] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:09:37] Reading known junctions from GTF file
[2018-10-13 09:09:40] Preparing reads
	 left reads: min. length=100, max. length=100, 918787 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 918565 kept reads (346 discarded)
[2018-10-13 09:10:06] Building transcriptome data files /scratch/8793138.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:10:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:15:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:15:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:15:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:15:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:16:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:16:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:16:24] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:16:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:16:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:16:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:16:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:17:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:17:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:17:13] Searching for junctions via segment mapping
[2018-10-13 09:19:07] Retrieving sequences for splices
[2018-10-13 09:20:13] Indexing splices
[2018-10-13 09:20:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:20:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:20:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:20:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:20:35] Joining segment hits
[2018-10-13 09:21:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:21:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:21:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:21:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:22:01] Joining segment hits
[2018-10-13 09:23:17] Reporting output tracks
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[2018-10-13 09:27:32] A summary of the alignment counts can be found in /scratch/8793138.1.p8/tophat2/align_summary.txt
[2018-10-13 09:27:32] Run complete: 00:17:57 elapsed