[2018-10-13 06:04:48] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:04:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:04:49] Checking for Bowtie index files (genome)..
[2018-10-13 06:04:49] Checking for reference FASTA file
[2018-10-13 06:04:49] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:04:50] Reading known junctions from GTF file
[2018-10-13 06:04:53] Preparing reads
	 left reads: min. length=100, max. length=100, 468891 kept reads (277 discarded)
	right reads: min. length=100, max. length=100, 468621 kept reads (547 discarded)
[2018-10-13 06:05:06] Building transcriptome data files /scratch/8793044.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:05:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:09:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:10:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:10:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:10:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:11:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:11:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:11:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:11:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:11:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:12:07] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:12:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:12:17] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:12:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:12:28] Searching for junctions via segment mapping
[2018-10-13 06:13:51] Retrieving sequences for splices
[2018-10-13 06:14:58] Indexing splices
[2018-10-13 06:15:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:15:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:15:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:15:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:15:20] Joining segment hits
[2018-10-13 06:16:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:16:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:16:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:16:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:16:45] Joining segment hits
[2018-10-13 06:18:02] Reporting output tracks
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[2018-10-13 06:19:57] A summary of the alignment counts can be found in /scratch/8793044.1.p16/tophat2/align_summary.txt
[2018-10-13 06:19:57] Run complete: 00:15:08 elapsed