[2018-10-12 21:38:08] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:38:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:38:08] Checking for Bowtie index files (genome)..
[2018-10-12 21:38:08] Checking for reference FASTA file
[2018-10-12 21:38:08] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:38:10] Reading known junctions from GTF file
[2018-10-12 21:38:12] Preparing reads
	 left reads: min. length=100, max. length=100, 386574 kept reads (263 discarded)
	right reads: min. length=100, max. length=100, 386224 kept reads (613 discarded)
[2018-10-12 21:38:24] Building transcriptome data files /scratch/8792766.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:38:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:43:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:43:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:44:02] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:44:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:44:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:44:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:44:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:45:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:45:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:45:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:45:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:45:35] Searching for junctions via segment mapping
[2018-10-12 21:46:57] Retrieving sequences for splices
[2018-10-12 21:48:04] Indexing splices
[2018-10-12 21:48:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:48:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:48:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:48:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:48:23] Joining segment hits
[2018-10-12 21:49:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:49:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:49:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:49:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:49:43] Joining segment hits
[2018-10-12 21:50:54] Reporting output tracks
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[2018-10-12 21:52:42] A summary of the alignment counts can be found in /scratch/8792766.1.p16/tophat2/align_summary.txt
[2018-10-12 21:52:42] Run complete: 00:14:33 elapsed