[2020-03-09 05:48:22] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:48:22] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:48:22] Checking for Bowtie index files (genome)..
[2020-03-09 05:48:22] Checking for reference FASTA file
[2020-03-09 05:48:22] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:48:24] Reading known junctions from GTF file
[2020-03-09 05:48:26] Preparing reads
	 left reads: min. length=75, max. length=75, 26807379 kept reads (16656 discarded)
[2020-03-09 05:53:52] Building transcriptome data files /scratch/3763314.1.p8/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 05:54:00] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 05:58:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:04:30] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:04:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:12:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:13:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:14:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:14:57] Searching for junctions via segment mapping
[2020-03-09 06:16:28] Retrieving sequences for splices
[2020-03-09 06:17:28] Indexing splices
[2020-03-09 06:17:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:17:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:18:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:18:20] Joining segment hits
[2020-03-09 06:19:40] Reporting output tracks
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[2020-03-09 06:27:48] A summary of the alignment counts can be found in /scratch/3763314.1.p8/tophat2/align_summary.txt
[2020-03-09 06:27:48] Run complete: 00:39:25 elapsed