[2018-10-13 04:22:37] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:22:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:22:37] Checking for Bowtie index files (genome)..
[2018-10-13 04:22:37] Checking for reference FASTA file
[2018-10-13 04:22:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:22:39] Reading known junctions from GTF file
[2018-10-13 04:22:42] Preparing reads
	 left reads: min. length=100, max. length=100, 456999 kept reads (51 discarded)
	right reads: min. length=100, max. length=100, 456882 kept reads (168 discarded)
[2018-10-13 04:22:55] Building transcriptome data files /scratch/8792991.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:23:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:27:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:28:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:28:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:28:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:28:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:28:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:28:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:29:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:29:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:29:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:29:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:29:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:29:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:29:35] Searching for junctions via segment mapping
[2018-10-13 04:31:32] Retrieving sequences for splices
[2018-10-13 04:32:39] Indexing splices
[2018-10-13 04:32:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:32:52] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:32:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:32:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:33:00] Joining segment hits
[2018-10-13 04:34:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:34:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:34:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:34:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:34:25] Joining segment hits
[2018-10-13 04:35:39] Reporting output tracks
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[2018-10-13 04:40:18] A summary of the alignment counts can be found in /scratch/8792991.1.p8/tophat2/align_summary.txt
[2018-10-13 04:40:18] Run complete: 00:17:41 elapsed