[2020-03-09 05:49:17] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:49:17] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:49:18] Checking for Bowtie index files (genome)..
[2020-03-09 05:49:18] Checking for reference FASTA file
[2020-03-09 05:49:18] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:49:19] Reading known junctions from GTF file
[2020-03-09 05:49:21] Preparing reads
	 left reads: min. length=75, max. length=75, 25368672 kept reads (14074 discarded)
[2020-03-09 05:54:21] Building transcriptome data files /scratch/3763316.1.p16/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 05:54:30] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 05:58:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:04:32] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:04:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:12:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:12:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:13:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:14:35] Searching for junctions via segment mapping
[2020-03-09 06:16:05] Retrieving sequences for splices
[2020-03-09 06:17:05] Indexing splices
[2020-03-09 06:17:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:17:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:17:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:17:54] Joining segment hits
[2020-03-09 06:19:13] Reporting output tracks
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[2020-03-09 06:35:02] A summary of the alignment counts can be found in /scratch/3763316.1.p16/tophat2/align_summary.txt
[2020-03-09 06:35:02] Run complete: 00:45:45 elapsed