[2020-03-09 06:52:13] Beginning TopHat run (v2.1.1)
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[2020-03-09 06:52:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 06:52:14] Checking for Bowtie index files (genome)..
[2020-03-09 06:52:14] Checking for reference FASTA file
[2020-03-09 06:52:14] Generating SAM header for Bowtie2Index/genome
[2020-03-09 06:52:16] Reading known junctions from GTF file
[2020-03-09 06:52:18] Preparing reads
	 left reads: min. length=75, max. length=75, 25926896 kept reads (11309 discarded)
[2020-03-09 06:57:26] Building transcriptome data files /scratch/3763320.1.p16/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:57:35] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 07:01:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 07:08:32] Resuming TopHat pipeline with unmapped reads
[2020-03-09 07:08:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 07:14:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 07:15:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 07:16:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 07:16:55] Searching for junctions via segment mapping
[2020-03-09 07:18:36] Retrieving sequences for splices
[2020-03-09 07:19:36] Indexing splices
[2020-03-09 07:19:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:20:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:20:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:20:21] Joining segment hits
[2020-03-09 07:21:40] Reporting output tracks
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[2020-03-09 07:40:38] A summary of the alignment counts can be found in /scratch/3763320.1.p16/tophat2/align_summary.txt
[2020-03-09 07:40:38] Run complete: 00:48:24 elapsed