[2018-10-12 22:46:42] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:46:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:46:42] Checking for Bowtie index files (genome)..
[2018-10-12 22:46:42] Checking for reference FASTA file
[2018-10-12 22:46:42] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:46:44] Reading known junctions from GTF file
[2018-10-12 22:46:47] Preparing reads
	 left reads: min. length=100, max. length=100, 360223 kept reads (182 discarded)
	right reads: min. length=100, max. length=100, 359754 kept reads (651 discarded)
[2018-10-12 22:46:56] Building transcriptome data files /scratch/8792810.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:47:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:51:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:52:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:52:30] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:52:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:52:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:52:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:53:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:53:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:53:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:53:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:53:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:53:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:53:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:53:51] Searching for junctions via segment mapping
[2018-10-12 22:55:10] Retrieving sequences for splices
[2018-10-12 22:56:17] Indexing splices
[2018-10-12 22:56:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:56:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:56:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:56:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:56:38] Joining segment hits
[2018-10-12 22:57:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:57:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:57:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:58:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:58:03] Joining segment hits
[2018-10-12 22:59:18] Reporting output tracks
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[2018-10-12 23:01:01] A summary of the alignment counts can be found in /scratch/8792810.1.p16/tophat2/align_summary.txt
[2018-10-12 23:01:01] Run complete: 00:14:18 elapsed