[2020-03-09 05:48:27] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:48:27] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:48:27] Checking for Bowtie index files (genome)..
[2020-03-09 05:48:27] Checking for reference FASTA file
[2020-03-09 05:48:27] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:48:34] Reading known junctions from GTF file
[2020-03-09 05:48:38] Preparing reads
	 left reads: min. length=75, max. length=75, 27162282 kept reads (14633 discarded)
[2020-03-09 06:00:08] Building transcriptome data files /scratch/3763313.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:00:27] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:08:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:19:09] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:19:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:36:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:38:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:40:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:42:46] Searching for junctions via segment mapping
[2020-03-09 06:47:11] Retrieving sequences for splices
[2020-03-09 06:49:42] Indexing splices
[2020-03-09 06:50:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:50:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:50:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:51:16] Joining segment hits
[2020-03-09 06:54:56] Reporting output tracks
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[2020-03-09 07:19:02] A summary of the alignment counts can be found in /scratch/3763313.1.linga/tophat2/align_summary.txt
[2020-03-09 07:19:02] Run complete: 01:30:34 elapsed