[2018-10-13 05:14:13] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:14:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:14:13] Checking for Bowtie index files (genome)..
[2018-10-13 05:14:13] Checking for reference FASTA file
[2018-10-13 05:14:13] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:14:15] Reading known junctions from GTF file
[2018-10-13 05:14:17] Preparing reads
	 left reads: min. length=100, max. length=100, 199582 kept reads (202 discarded)
	right reads: min. length=100, max. length=100, 199394 kept reads (390 discarded)
[2018-10-13 05:14:23] Building transcriptome data files /scratch/8793017.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:14:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:20:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:20:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:20:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:20:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:20:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:20:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:21:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:21:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:21:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:21:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:21:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:21:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:21:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:21:41] Searching for junctions via segment mapping
[2018-10-13 05:23:04] Retrieving sequences for splices
[2018-10-13 05:24:16] Indexing splices
[2018-10-13 05:24:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:24:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:24:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:24:34] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:24:36] Joining segment hits
[2018-10-13 05:25:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:25:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:25:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:25:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:26:00] Joining segment hits
[2018-10-13 05:27:15] Reporting output tracks
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[2018-10-13 05:29:00] A summary of the alignment counts can be found in /scratch/8793017.1.c/tophat2/align_summary.txt
[2018-10-13 05:29:00] Run complete: 00:14:47 elapsed