[2018-10-13 09:46:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:46:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:46:40] Checking for Bowtie index files (genome)..
[2018-10-13 09:46:40] Checking for reference FASTA file
[2018-10-13 09:46:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:46:43] Reading known junctions from GTF file
[2018-10-13 09:46:45] Preparing reads
	 left reads: min. length=100, max. length=100, 1551687 kept reads (121 discarded)
	right reads: min. length=100, max. length=100, 1550896 kept reads (912 discarded)
[2018-10-13 09:47:30] Building transcriptome data files /scratch/8793155.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:47:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:52:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:53:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:53:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:53:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:54:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:54:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:54:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:54:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:54:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:55:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:55:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:55:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:55:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:55:32] Searching for junctions via segment mapping
[2018-10-13 09:57:49] Retrieving sequences for splices
[2018-10-13 09:58:56] Indexing splices
[2018-10-13 09:59:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:59:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:59:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:59:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:59:21] Joining segment hits
[2018-10-13 10:00:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:00:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:00:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:00:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:00:51] Joining segment hits
[2018-10-13 10:02:09] Reporting output tracks
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[2018-10-13 10:09:25] A summary of the alignment counts can be found in /scratch/8793155.1.p16/tophat2/align_summary.txt
[2018-10-13 10:09:25] Run complete: 00:22:44 elapsed