[2018-10-13 15:23:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:23:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:23:58] Checking for Bowtie index files (genome)..
[2018-10-13 15:23:58] Checking for reference FASTA file
[2018-10-13 15:23:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:24:00] Reading known junctions from GTF file
[2018-10-13 15:24:02] Preparing reads
	 left reads: min. length=100, max. length=100, 329405 kept reads (211 discarded)
	right reads: min. length=100, max. length=100, 329177 kept reads (439 discarded)
[2018-10-13 15:24:11] Building transcriptome data files /scratch/8793318.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:24:21] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:29:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:29:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:29:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:29:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:29:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:29:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:30:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:30:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:30:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:30:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:30:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:30:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:30:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:30:46] Searching for junctions via segment mapping
[2018-10-13 15:32:10] Retrieving sequences for splices
[2018-10-13 15:33:16] Indexing splices
[2018-10-13 15:33:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:33:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:33:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:33:34] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:33:36] Joining segment hits
[2018-10-13 15:34:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:34:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:34:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:34:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:34:54] Joining segment hits
[2018-10-13 15:36:04] Reporting output tracks
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[2018-10-13 15:38:00] A summary of the alignment counts can be found in /scratch/8793318.1.p16/tophat2/align_summary.txt
[2018-10-13 15:38:00] Run complete: 00:14:02 elapsed