[2018-10-13 07:06:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:06:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:06:15] Checking for Bowtie index files (genome)..
[2018-10-13 07:06:15] Checking for reference FASTA file
[2018-10-13 07:06:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:06:17] Reading known junctions from GTF file
[2018-10-13 07:06:19] Preparing reads
	 left reads: min. length=100, max. length=100, 1041270 kept reads (78 discarded)
	right reads: min. length=100, max. length=100, 1040869 kept reads (479 discarded)
[2018-10-13 07:06:49] Building transcriptome data files /scratch/8793078.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:07:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:11:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:12:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:12:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:12:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:12:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:13:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:13:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:13:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:13:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:13:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:13:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:13:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:13:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:13:58] Searching for junctions via segment mapping
[2018-10-13 07:15:53] Retrieving sequences for splices
[2018-10-13 07:16:59] Indexing splices
[2018-10-13 07:17:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:17:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:17:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:17:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:17:21] Joining segment hits
[2018-10-13 07:18:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:18:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:18:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:18:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:18:48] Joining segment hits
[2018-10-13 07:20:04] Reporting output tracks
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[2018-10-13 07:24:41] A summary of the alignment counts can be found in /scratch/8793078.1.p16/tophat2/align_summary.txt
[2018-10-13 07:24:41] Run complete: 00:18:26 elapsed