[2020-03-09 05:48:40] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:48:40] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:48:41] Checking for Bowtie index files (genome)..
[2020-03-09 05:48:41] Checking for reference FASTA file
[2020-03-09 05:48:41] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:48:46] Reading known junctions from GTF file
[2020-03-09 05:48:50] Preparing reads
	 left reads: min. length=75, max. length=75, 27012546 kept reads (15600 discarded)
[2020-03-09 05:58:36] Building transcriptome data files /scratch/3763305.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 05:58:57] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:06:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:16:15] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:16:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:34:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:36:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:38:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:40:38] Searching for junctions via segment mapping
[2020-03-09 06:44:33] Retrieving sequences for splices
[2020-03-09 06:46:43] Indexing splices
[2020-03-09 06:47:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:47:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:47:59] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:48:23] Joining segment hits
[2020-03-09 06:51:36] Reporting output tracks
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[2020-03-09 07:12:49] A summary of the alignment counts can be found in /scratch/3763305.1.linga/tophat2/align_summary.txt
[2020-03-09 07:12:49] Run complete: 01:24:08 elapsed