[2020-03-09 05:48:34] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:48:34] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:48:35] Checking for Bowtie index files (genome)..
[2020-03-09 05:48:35] Checking for reference FASTA file
[2020-03-09 05:48:35] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:48:39] Reading known junctions from GTF file
[2020-03-09 05:48:43] Preparing reads
	 left reads: min. length=75, max. length=75, 33189124 kept reads (20732 discarded)
[2020-03-09 06:00:21] Building transcriptome data files /scratch/3763309.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:00:39] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:07:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:20:06] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:20:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:40:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:43:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:45:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:47:44] Searching for junctions via segment mapping
[2020-03-09 06:51:48] Retrieving sequences for splices
[2020-03-09 06:54:03] Indexing splices
[2020-03-09 06:54:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:55:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:55:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:56:09] Joining segment hits
[2020-03-09 06:59:17] Reporting output tracks
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[2020-03-09 07:22:53] A summary of the alignment counts can be found in /scratch/3763309.1.linga/tophat2/align_summary.txt
[2020-03-09 07:22:53] Run complete: 01:34:19 elapsed