[2018-10-13 17:26:06] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:26:06] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:26:06] Checking for Bowtie index files (genome)..
[2018-10-13 17:26:06] Checking for reference FASTA file
[2018-10-13 17:26:06] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:26:08] Reading known junctions from GTF file
[2018-10-13 17:26:10] Preparing reads
	 left reads: min. length=100, max. length=100, 207548 kept reads (211 discarded)
	right reads: min. length=100, max. length=100, 207401 kept reads (358 discarded)
[2018-10-13 17:26:16] Building transcriptome data files /scratch/8793396.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:26:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:31:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:31:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:31:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:31:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:31:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:31:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:32:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:32:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:32:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:32:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:32:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:32:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:32:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:32:37] Searching for junctions via segment mapping
[2018-10-13 17:33:51] Retrieving sequences for splices
[2018-10-13 17:34:57] Indexing splices
[2018-10-13 17:35:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:35:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:35:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:35:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:35:16] Joining segment hits
[2018-10-13 17:36:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:36:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:36:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:36:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:36:33] Joining segment hits
[2018-10-13 17:37:42] Reporting output tracks
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[2018-10-13 17:39:08] A summary of the alignment counts can be found in /scratch/8793396.1.p16/tophat2/align_summary.txt
[2018-10-13 17:39:08] Run complete: 00:13:02 elapsed