[2018-10-13 11:08:36] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:08:36] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:08:36] Checking for Bowtie index files (genome)..
[2018-10-13 11:08:36] Checking for reference FASTA file
[2018-10-13 11:08:36] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:08:38] Reading known junctions from GTF file
[2018-10-13 11:08:40] Preparing reads
	 left reads: min. length=100, max. length=100, 2934882 kept reads (281 discarded)
	right reads: min. length=100, max. length=100, 2934289 kept reads (874 discarded)
[2018-10-13 11:09:51] Building transcriptome data files /scratch/8793195.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:10:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:14:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:17:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:19:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:19:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:20:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:20:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:20:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:20:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:21:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:21:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:22:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:22:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:22:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:22:49] Searching for junctions via segment mapping
[2018-10-13 11:32:14] Retrieving sequences for splices
[2018-10-13 11:33:21] Indexing splices
[2018-10-13 11:33:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:33:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:33:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:34:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:34:15] Joining segment hits
[2018-10-13 11:35:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:35:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:35:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:36:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:36:18] Joining segment hits
[2018-10-13 11:37:41] Reporting output tracks
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[2018-10-13 12:15:04] A summary of the alignment counts can be found in /scratch/8793195.1.p16/tophat2/align_summary.txt
[2018-10-13 12:15:04] Run complete: 01:06:27 elapsed