[2018-10-13 03:35:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:35:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:35:53] Checking for Bowtie index files (genome)..
[2018-10-13 03:35:53] Checking for reference FASTA file
[2018-10-13 03:35:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:35:55] Reading known junctions from GTF file
[2018-10-13 03:35:57] Preparing reads
	 left reads: min. length=100, max. length=100, 589397 kept reads (134 discarded)
	right reads: min. length=100, max. length=100, 589251 kept reads (280 discarded)
[2018-10-13 03:36:14] Building transcriptome data files /scratch/8792962.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:36:25] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:41:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:41:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:42:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:42:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:42:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:42:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:42:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:43:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:43:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:43:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:43:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:43:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:43:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:43:45] Searching for junctions via segment mapping
[2018-10-13 03:47:10] Retrieving sequences for splices
[2018-10-13 03:48:18] Indexing splices
[2018-10-13 03:48:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:48:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:48:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:48:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:48:46] Joining segment hits
[2018-10-13 03:50:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:50:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:50:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:50:13] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:50:17] Joining segment hits
[2018-10-13 03:51:32] Reporting output tracks
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[2018-10-13 04:00:44] A summary of the alignment counts can be found in /scratch/8792962.1.p16/tophat2/align_summary.txt
[2018-10-13 04:00:44] Run complete: 00:24:50 elapsed