[2018-10-13 05:05:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:05:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:05:15] Checking for Bowtie index files (genome)..
[2018-10-13 05:05:15] Checking for reference FASTA file
[2018-10-13 05:05:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:05:17] Reading known junctions from GTF file
[2018-10-13 05:05:20] Preparing reads
	 left reads: min. length=100, max. length=100, 612586 kept reads (148 discarded)
	right reads: min. length=100, max. length=100, 612423 kept reads (311 discarded)
[2018-10-13 05:05:35] Building transcriptome data files /scratch/8793013.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:05:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:10:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:11:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:11:53] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:11:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:12:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:12:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:12:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:12:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:12:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:12:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:12:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:12:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:13:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:13:10] Searching for junctions via segment mapping
[2018-10-13 05:16:20] Retrieving sequences for splices
[2018-10-13 05:17:27] Indexing splices
[2018-10-13 05:17:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:17:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:17:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:17:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:17:56] Joining segment hits
[2018-10-13 05:19:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:19:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:19:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:19:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:19:29] Joining segment hits
[2018-10-13 05:20:44] Reporting output tracks
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[2018-10-13 05:31:30] A summary of the alignment counts can be found in /scratch/8793013.1.p8/tophat2/align_summary.txt
[2018-10-13 05:31:30] Run complete: 00:26:14 elapsed