[2020-03-09 05:49:24] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:49:24] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:49:24] Checking for Bowtie index files (genome)..
[2020-03-09 05:49:24] Checking for reference FASTA file
[2020-03-09 05:49:24] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:49:25] Reading known junctions from GTF file
[2020-03-09 05:49:27] Preparing reads
	 left reads: min. length=75, max. length=75, 27864059 kept reads (15632 discarded)
[2020-03-09 05:55:01] Building transcriptome data files /scratch/3763315.1.p16/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 05:55:10] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 05:59:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:06:01] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:06:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:12:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:13:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:14:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:15:26] Searching for junctions via segment mapping
[2020-03-09 06:16:59] Retrieving sequences for splices
[2020-03-09 06:17:59] Indexing splices
[2020-03-09 06:18:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:18:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:18:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:18:48] Joining segment hits
[2020-03-09 06:20:05] Reporting output tracks
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[2020-03-09 06:34:09] A summary of the alignment counts can be found in /scratch/3763315.1.p16/tophat2/align_summary.txt
[2020-03-09 06:34:09] Run complete: 00:44:45 elapsed