[2018-10-13 14:44:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:44:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:44:58] Checking for Bowtie index files (genome)..
[2018-10-13 14:44:58] Checking for reference FASTA file
[2018-10-13 14:44:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:45:00] Reading known junctions from GTF file
[2018-10-13 14:45:03] Preparing reads
	 left reads: min. length=100, max. length=100, 668352 kept reads (48 discarded)
	right reads: min. length=100, max. length=100, 668219 kept reads (181 discarded)
[2018-10-13 14:45:21] Building transcriptome data files /scratch/8793301.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:45:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:50:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:50:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:50:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:50:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:51:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:51:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:51:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:51:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:51:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:51:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:51:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:51:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:52:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:52:05] Searching for junctions via segment mapping
[2018-10-13 14:53:49] Retrieving sequences for splices
[2018-10-13 14:54:55] Indexing splices
[2018-10-13 14:55:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:55:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:55:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:55:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:55:15] Joining segment hits
[2018-10-13 14:56:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:56:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:56:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:56:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:56:40] Joining segment hits
[2018-10-13 14:57:54] Reporting output tracks
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[2018-10-13 15:01:05] A summary of the alignment counts can be found in /scratch/8793301.1.p16/tophat2/align_summary.txt
[2018-10-13 15:01:05] Run complete: 00:16:07 elapsed