[2018-10-13 11:41:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:41:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:41:53] Checking for Bowtie index files (genome)..
[2018-10-13 11:41:53] Checking for reference FASTA file
[2018-10-13 11:41:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:41:56] Reading known junctions from GTF file
[2018-10-13 11:41:58] Preparing reads
	 left reads: min. length=100, max. length=100, 885232 kept reads (87 discarded)
	right reads: min. length=100, max. length=100, 885030 kept reads (289 discarded)
[2018-10-13 11:42:22] Building transcriptome data files /scratch/8793213.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:42:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:47:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:47:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:48:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:48:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:48:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:48:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:48:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:48:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:48:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:49:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:49:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:49:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:49:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:49:37] Searching for junctions via segment mapping
[2018-10-13 11:51:12] Retrieving sequences for splices
[2018-10-13 11:52:18] Indexing splices
[2018-10-13 11:52:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:52:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:52:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:52:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:52:39] Joining segment hits
[2018-10-13 11:53:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:53:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:53:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:54:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:54:03] Joining segment hits
[2018-10-13 11:55:18] Reporting output tracks
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[2018-10-13 11:57:48] A summary of the alignment counts can be found in /scratch/8793213.1.p16/tophat2/align_summary.txt
[2018-10-13 11:57:48] Run complete: 00:15:54 elapsed