[2018-10-12 22:29:48] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:29:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:29:48] Checking for Bowtie index files (genome)..
[2018-10-12 22:29:48] Checking for reference FASTA file
[2018-10-12 22:29:48] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:29:50] Reading known junctions from GTF file
[2018-10-12 22:29:52] Preparing reads
	 left reads: min. length=100, max. length=100, 221728 kept reads (141 discarded)
	right reads: min. length=100, max. length=100, 221544 kept reads (325 discarded)
[2018-10-12 22:29:59] Building transcriptome data files /scratch/8792796.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:30:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:34:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:35:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:35:18] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:35:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:35:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:35:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:35:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:35:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:35:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:36:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:36:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:36:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:36:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:36:21] Searching for junctions via segment mapping
[2018-10-12 22:37:35] Retrieving sequences for splices
[2018-10-12 22:38:42] Indexing splices
[2018-10-12 22:38:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:38:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:38:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:38:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:39:02] Joining segment hits
[2018-10-12 22:40:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:40:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:40:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:40:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:40:19] Joining segment hits
[2018-10-12 22:41:29] Reporting output tracks
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[2018-10-12 22:42:58] A summary of the alignment counts can be found in /scratch/8792796.1.p16/tophat2/align_summary.txt
[2018-10-12 22:42:58] Run complete: 00:13:09 elapsed