[2018-10-12 21:21:06] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:21:06] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:21:06] Checking for Bowtie index files (genome)..
[2018-10-12 21:21:06] Checking for reference FASTA file
[2018-10-12 21:21:06] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:21:07] Reading known junctions from GTF file
[2018-10-12 21:21:10] Preparing reads
	 left reads: min. length=100, max. length=100, 437206 kept reads (226 discarded)
	right reads: min. length=100, max. length=100, 436797 kept reads (635 discarded)
[2018-10-12 21:21:22] Building transcriptome data files /scratch/8792750.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:21:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:26:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:26:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:27:04] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:27:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:27:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:27:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:27:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:27:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:27:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:28:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:28:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:28:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:28:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:28:29] Searching for junctions via segment mapping
[2018-10-12 21:29:55] Retrieving sequences for splices
[2018-10-12 21:31:02] Indexing splices
[2018-10-12 21:31:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:31:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:31:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:31:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:31:22] Joining segment hits
[2018-10-12 21:32:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:32:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:32:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:32:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:32:47] Joining segment hits
[2018-10-12 21:34:03] Reporting output tracks
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[2018-10-12 21:35:53] A summary of the alignment counts can be found in /scratch/8792750.1.p16/tophat2/align_summary.txt
[2018-10-12 21:35:53] Run complete: 00:14:47 elapsed