[2018-10-13 03:14:52] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:14:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:14:52] Checking for Bowtie index files (genome)..
[2018-10-13 03:14:52] Checking for reference FASTA file
[2018-10-13 03:14:52] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:14:54] Reading known junctions from GTF file
[2018-10-13 03:14:57] Preparing reads
	 left reads: min. length=100, max. length=100, 300756 kept reads (336 discarded)
	right reads: min. length=100, max. length=100, 300537 kept reads (555 discarded)
[2018-10-13 03:15:05] Building transcriptome data files /scratch/8792949.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:15:15] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:20:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:20:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:20:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:20:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:21:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:21:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:21:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:21:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:21:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:22:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:22:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:22:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:22:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:22:23] Searching for junctions via segment mapping
[2018-10-13 03:23:37] Retrieving sequences for splices
[2018-10-13 03:24:44] Indexing splices
[2018-10-13 03:24:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:24:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:25:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:25:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:25:04] Joining segment hits
[2018-10-13 03:26:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:26:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:26:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:26:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:26:23] Joining segment hits
[2018-10-13 03:27:34] Reporting output tracks
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[2018-10-13 03:29:07] A summary of the alignment counts can be found in /scratch/8792949.1.p8/tophat2/align_summary.txt
[2018-10-13 03:29:07] Run complete: 00:14:15 elapsed