[2018-10-13 12:22:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:22:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:22:31] Checking for Bowtie index files (genome)..
[2018-10-13 12:22:31] Checking for reference FASTA file
[2018-10-13 12:22:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:22:33] Reading known junctions from GTF file
[2018-10-13 12:22:35] Preparing reads
	 left reads: min. length=100, max. length=100, 712139 kept reads (82 discarded)
	right reads: min. length=100, max. length=100, 711991 kept reads (230 discarded)
[2018-10-13 12:22:56] Building transcriptome data files /scratch/8793229.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:23:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:27:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:28:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:28:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:28:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:28:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:28:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:29:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:29:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:29:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:29:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:29:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:29:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:29:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:29:46] Searching for junctions via segment mapping
[2018-10-13 12:31:48] Retrieving sequences for splices
[2018-10-13 12:32:54] Indexing splices
[2018-10-13 12:33:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:33:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:33:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:33:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:33:16] Joining segment hits
[2018-10-13 12:34:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:34:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:34:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:34:38] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:34:41] Joining segment hits
[2018-10-13 12:35:55] Reporting output tracks
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[2018-10-13 12:40:46] A summary of the alignment counts can be found in /scratch/8793229.1.p16/tophat2/align_summary.txt
[2018-10-13 12:40:46] Run complete: 00:18:14 elapsed