[2018-10-13 13:33:17] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:33:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:33:17] Checking for Bowtie index files (genome)..
[2018-10-13 13:33:17] Checking for reference FASTA file
[2018-10-13 13:33:17] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:33:19] Reading known junctions from GTF file
[2018-10-13 13:33:21] Preparing reads
	 left reads: min. length=100, max. length=100, 1129454 kept reads (60 discarded)
	right reads: min. length=100, max. length=100, 1129235 kept reads (279 discarded)
[2018-10-13 13:33:54] Building transcriptome data files /scratch/8793263.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:34:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:38:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:39:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:40:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:40:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:40:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:40:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:40:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:40:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:40:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:41:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:41:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:41:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:41:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:41:37] Searching for junctions via segment mapping
[2018-10-13 13:44:12] Retrieving sequences for splices
[2018-10-13 13:45:19] Indexing splices
[2018-10-13 13:45:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:45:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:45:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:45:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:45:44] Joining segment hits
[2018-10-13 13:47:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:47:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:47:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:47:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:47:13] Joining segment hits
[2018-10-13 13:48:29] Reporting output tracks
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[2018-10-13 13:56:42] A summary of the alignment counts can be found in /scratch/8793263.1.p16/tophat2/align_summary.txt
[2018-10-13 13:56:42] Run complete: 00:23:25 elapsed