[2018-10-12 22:29:46] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:29:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:29:46] Checking for Bowtie index files (genome)..
[2018-10-12 22:29:46] Checking for reference FASTA file
[2018-10-12 22:29:46] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:29:48] Reading known junctions from GTF file
[2018-10-12 22:29:51] Preparing reads
	 left reads: min. length=100, max. length=100, 294836 kept reads (206 discarded)
	right reads: min. length=100, max. length=100, 294481 kept reads (561 discarded)
[2018-10-12 22:29:59] Building transcriptome data files /scratch/8792795.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:30:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:34:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:35:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:35:31] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:35:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:35:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:35:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:36:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:36:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:36:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:36:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:36:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:36:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:36:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:36:49] Searching for junctions via segment mapping
[2018-10-12 22:38:06] Retrieving sequences for splices
[2018-10-12 22:39:13] Indexing splices
[2018-10-12 22:39:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:39:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:39:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:39:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:39:33] Joining segment hits
[2018-10-12 22:40:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:40:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:40:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:40:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:40:52] Joining segment hits
[2018-10-12 22:42:02] Reporting output tracks
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[2018-10-12 22:43:38] A summary of the alignment counts can be found in /scratch/8792795.1.p8/tophat2/align_summary.txt
[2018-10-12 22:43:38] Run complete: 00:13:51 elapsed