[2018-10-13 04:11:37] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:11:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:11:37] Checking for Bowtie index files (genome)..
[2018-10-13 04:11:37] Checking for reference FASTA file
[2018-10-13 04:11:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:11:39] Reading known junctions from GTF file
[2018-10-13 04:11:41] Preparing reads
	 left reads: min. length=100, max. length=100, 916653 kept reads (277 discarded)
	right reads: min. length=100, max. length=100, 916504 kept reads (426 discarded)
[2018-10-13 04:12:07] Building transcriptome data files /scratch/8792984.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:12:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:17:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:17:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:18:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:18:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:19:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:19:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:19:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:19:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:19:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:20:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:20:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:20:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:20:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:20:36] Searching for junctions via segment mapping
[2018-10-13 04:25:41] Retrieving sequences for splices
[2018-10-13 04:26:48] Indexing splices
[2018-10-13 04:27:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:27:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:27:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:27:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:27:23] Joining segment hits
[2018-10-13 04:28:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:28:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:28:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:28:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:29:02] Joining segment hits
[2018-10-13 04:30:19] Reporting output tracks
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[2018-10-13 04:40:00] A summary of the alignment counts can be found in /scratch/8792984.1.p16/tophat2/align_summary.txt
[2018-10-13 04:40:00] Run complete: 00:28:23 elapsed