[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 22:46:46] Preparing reads
	 left reads: min. length=100, max. length=100, 478794 kept reads (186 discarded)
	right reads: min. length=100, max. length=100, 478501 kept reads (479 discarded)
[2018-10-12 22:47:01] Building transcriptome data files /scratch/8792809.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:47:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:51:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:52:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:52:45] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:52:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:53:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:53:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:53:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:53:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:53:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:53:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:54:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:54:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:54:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:54:19] Searching for junctions via segment mapping
[2018-10-12 22:55:43] Retrieving sequences for splices
[2018-10-12 22:56:49] Indexing splices
[2018-10-12 22:57:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:57:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:57:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:57:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:57:09] Joining segment hits
[2018-10-12 22:58:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:58:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:58:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:58:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:58:34] Joining segment hits
[2018-10-12 22:59:51] Reporting output tracks
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[2018-10-12 23:01:58] A summary of the alignment counts can be found in /scratch/8792809.1.p8/tophat2/align_summary.txt
[2018-10-12 23:01:58] Run complete: 00:15:15 elapsed