[2018-10-13 13:59:18] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:59:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:59:18] Checking for Bowtie index files (genome)..
[2018-10-13 13:59:18] Checking for reference FASTA file
[2018-10-13 13:59:18] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:59:20] Reading known junctions from GTF file
[2018-10-13 13:59:22] Preparing reads
	 left reads: min. length=100, max. length=100, 711569 kept reads (74 discarded)
	right reads: min. length=100, max. length=100, 711352 kept reads (291 discarded)
[2018-10-13 13:59:38] Building transcriptome data files /scratch/8793277.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:59:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:04:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:04:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:05:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:05:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:05:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:05:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:05:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:06:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:06:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:06:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:06:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:06:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:06:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:06:51] Searching for junctions via segment mapping
[2018-10-13 14:08:22] Retrieving sequences for splices
[2018-10-13 14:09:29] Indexing splices
[2018-10-13 14:09:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:09:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:09:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:09:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:09:49] Joining segment hits
[2018-10-13 14:11:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:11:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:11:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:11:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:11:13] Joining segment hits
[2018-10-13 14:12:27] Reporting output tracks
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[2018-10-13 14:14:38] A summary of the alignment counts can be found in /scratch/8793277.1.p16/tophat2/align_summary.txt
[2018-10-13 14:14:38] Run complete: 00:15:20 elapsed