[2018-10-13 09:11:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:11:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:11:30] Checking for Bowtie index files (genome)..
[2018-10-13 09:11:30] Checking for reference FASTA file
[2018-10-13 09:11:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:11:32] Reading known junctions from GTF file
[2018-10-13 09:11:35] Preparing reads
	 left reads: min. length=100, max. length=100, 945678 kept reads (528 discarded)
	right reads: min. length=100, max. length=100, 945463 kept reads (743 discarded)
[2018-10-13 09:11:59] Building transcriptome data files /scratch/8793140.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:12:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:16:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:17:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:18:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:18:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:19:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:19:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:19:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:19:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:19:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:20:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:20:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:20:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:21:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:21:09] Searching for junctions via segment mapping
[2018-10-13 09:26:52] Retrieving sequences for splices
[2018-10-13 09:27:59] Indexing splices
[2018-10-13 09:28:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:28:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:28:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:28:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:28:34] Joining segment hits
[2018-10-13 09:29:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:29:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:30:04] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:30:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:30:16] Joining segment hits
[2018-10-13 09:31:34] Reporting output tracks
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[2018-10-13 09:43:19] A summary of the alignment counts can be found in /scratch/8793140.1.p16/tophat2/align_summary.txt
[2018-10-13 09:43:19] Run complete: 00:31:49 elapsed