[2018-10-13 01:23:19] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:23:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:23:20] Checking for Bowtie index files (genome)..
[2018-10-13 01:23:20] Checking for reference FASTA file
[2018-10-13 01:23:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:23:22] Reading known junctions from GTF file
[2018-10-13 01:23:24] Preparing reads
	 left reads: min. length=100, max. length=100, 204162 kept reads (103 discarded)
	right reads: min. length=100, max. length=100, 203993 kept reads (272 discarded)
[2018-10-13 01:23:31] Building transcriptome data files /scratch/8792885.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:23:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:28:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:28:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:28:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:28:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:29:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:29:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:29:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:29:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:29:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:29:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:29:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:29:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:29:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:29:45] Searching for junctions via segment mapping
[2018-10-13 01:30:58] Retrieving sequences for splices
[2018-10-13 01:32:04] Indexing splices
[2018-10-13 01:32:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:32:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:32:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:32:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:32:23] Joining segment hits
[2018-10-13 01:33:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:33:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:33:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:33:38] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:33:39] Joining segment hits
[2018-10-13 01:34:48] Reporting output tracks
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[2018-10-13 01:36:13] A summary of the alignment counts can be found in /scratch/8792885.1.p8/tophat2/align_summary.txt
[2018-10-13 01:36:13] Run complete: 00:12:53 elapsed