[2018-10-12 23:03:27] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:03:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:03:27] Checking for Bowtie index files (genome)..
[2018-10-12 23:03:27] Checking for reference FASTA file
[2018-10-12 23:03:27] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:03:29] Reading known junctions from GTF file
[2018-10-12 23:03:32] Preparing reads
	 left reads: min. length=100, max. length=100, 228226 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 228054 kept reads (296 discarded)
[2018-10-12 23:03:38] Building transcriptome data files /scratch/8792820.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:03:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:08:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:08:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:08:57] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:08:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:09:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:09:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:09:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:09:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:09:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:09:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:09:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:09:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:09:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:09:58] Searching for junctions via segment mapping
[2018-10-12 23:11:13] Retrieving sequences for splices
[2018-10-12 23:12:20] Indexing splices
[2018-10-12 23:12:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:12:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:12:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:12:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:12:39] Joining segment hits
[2018-10-12 23:13:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:13:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:13:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:13:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:13:56] Joining segment hits
[2018-10-12 23:15:05] Reporting output tracks
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[2018-10-12 23:16:34] A summary of the alignment counts can be found in /scratch/8792820.1.p16/tophat2/align_summary.txt
[2018-10-12 23:16:34] Run complete: 00:13:07 elapsed