[2018-10-13 14:32:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:32:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:32:44] Checking for Bowtie index files (genome)..
[2018-10-13 14:32:44] Checking for reference FASTA file
[2018-10-13 14:32:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:32:46] Reading known junctions from GTF file
[2018-10-13 14:32:48] Preparing reads
	 left reads: min. length=100, max. length=100, 2520416 kept reads (608 discarded)
	right reads: min. length=100, max. length=100, 2519888 kept reads (1136 discarded)
[2018-10-13 14:33:51] Building transcriptome data files /scratch/8793294.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:34:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:38:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:41:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:43:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:43:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:44:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:45:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:45:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:45:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:45:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:46:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:46:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:47:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:47:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:47:48] Searching for junctions via segment mapping
[2018-10-13 14:58:45] Retrieving sequences for splices
[2018-10-13 14:59:52] Indexing splices
[2018-10-13 15:00:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:00:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:00:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:00:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:00:56] Joining segment hits
[2018-10-13 15:02:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:02:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:02:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:02:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:03:10] Joining segment hits
[2018-10-13 15:04:33] Reporting output tracks
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[2018-10-13 15:45:14] A summary of the alignment counts can be found in /scratch/8793294.1.p8/tophat2/align_summary.txt
[2018-10-13 15:45:14] Run complete: 01:12:30 elapsed