[2020-03-09 06:46:19] Beginning TopHat run (v2.1.1)
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[2020-03-09 06:46:19] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 06:46:21] Checking for Bowtie index files (genome)..
[2020-03-09 06:46:21] Checking for reference FASTA file
[2020-03-09 06:46:21] Generating SAM header for Bowtie2Index/genome
[2020-03-09 06:46:22] Reading known junctions from GTF file
[2020-03-09 06:46:28] Preparing reads
	 left reads: min. length=75, max. length=75, 27182134 kept reads (11734 discarded)
[2020-03-09 06:51:46] Building transcriptome data files /scratch/3763319.1.p8/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:51:55] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:55:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 07:02:55] Resuming TopHat pipeline with unmapped reads
[2020-03-09 07:02:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 07:09:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 07:10:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 07:11:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 07:12:06] Searching for junctions via segment mapping
[2020-03-09 07:13:49] Retrieving sequences for splices
[2020-03-09 07:14:49] Indexing splices
[2020-03-09 07:15:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:15:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:15:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:15:35] Joining segment hits
[2020-03-09 07:16:53] Reporting output tracks
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[2020-03-09 07:35:38] A summary of the alignment counts can be found in /scratch/3763319.1.p8/tophat2/align_summary.txt
[2020-03-09 07:35:38] Run complete: 00:49:18 elapsed