[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 15:24:03] Preparing reads
	 left reads: min. length=100, max. length=100, 295285 kept reads (242 discarded)
	right reads: min. length=100, max. length=100, 295115 kept reads (412 discarded)
[2018-10-13 15:24:11] Building transcriptome data files /scratch/8793317.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:24:22] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:29:04] 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 15:29:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:29:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:29:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:30:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:30:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:30:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:30:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:30:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:30:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:30:35] Searching for junctions via segment mapping
[2018-10-13 15:32:03] Retrieving sequences for splices
[2018-10-13 15:33:09] Indexing splices
[2018-10-13 15:33:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:33:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:33:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:33:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:33:30] 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 15:36:07] Reporting output tracks
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[2018-10-13 15:38:12] A summary of the alignment counts can be found in /scratch/8793317.1.p16/tophat2/align_summary.txt
[2018-10-13 15:38:12] Run complete: 00:14:13 elapsed