[2018-10-13 12:51:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:51:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:51:15] Checking for Bowtie index files (genome)..
[2018-10-13 12:51:15] Checking for reference FASTA file
[2018-10-13 12:51:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:51:17] Reading known junctions from GTF file
[2018-10-13 12:51:20] Preparing reads
	 left reads: min. length=100, max. length=100, 476935 kept reads (31 discarded)
	right reads: min. length=100, max. length=100, 476890 kept reads (76 discarded)
[2018-10-13 12:51:37] Building transcriptome data files /scratch/8793244.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:51:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:56:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:56:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:57:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:57:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:57:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:57:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:57:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:57:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:57:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:57:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:57:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:57:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:58:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:58:08] Searching for junctions via segment mapping
[2018-10-13 12:59:34] Retrieving sequences for splices
[2018-10-13 13:00:41] Indexing splices
[2018-10-13 13:00:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:00:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:00:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:00:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:01:00] Joining segment hits
[2018-10-13 13:02:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:02:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:02:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:02:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:02:17] Joining segment hits
[2018-10-13 13:03:26] Reporting output tracks
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[2018-10-13 13:05:22] A summary of the alignment counts can be found in /scratch/8793244.1.p16/tophat2/align_summary.txt
[2018-10-13 13:05:22] Run complete: 00:14:07 elapsed