[2018-10-13 02:40:59] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:40:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:40:59] Checking for Bowtie index files (genome)..
[2018-10-13 02:40:59] Checking for reference FASTA file
[2018-10-13 02:40:59] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:41:01] Reading known junctions from GTF file
[2018-10-13 02:41:03] Preparing reads
	 left reads: min. length=100, max. length=100, 429824 kept reads (390 discarded)
	right reads: min. length=100, max. length=100, 429867 kept reads (347 discarded)
[2018-10-13 02:41:16] Building transcriptome data files /scratch/8792925.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:41:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:46:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:46:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:46:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:46:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:47:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:47:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:47:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:47:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:47:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:48:10] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:48:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:48:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:48:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:48:31] Searching for junctions via segment mapping
[2018-10-13 02:49:55] Retrieving sequences for splices
[2018-10-13 02:51:02] Indexing splices
[2018-10-13 02:51:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:51:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:51:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:51:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:51:23] Joining segment hits
[2018-10-13 02:52:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:52:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:52:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:52:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:52:49] Joining segment hits
[2018-10-13 02:54:06] Reporting output tracks
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[2018-10-13 02:56:08] A summary of the alignment counts can be found in /scratch/8792925.1.p16/tophat2/align_summary.txt
[2018-10-13 02:56:08] Run complete: 00:15:09 elapsed