[2020-03-09 05:49:02] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:49:02] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:49:02] Checking for Bowtie index files (genome)..
[2020-03-09 05:49:02] Checking for reference FASTA file
[2020-03-09 05:49:02] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:49:07] Reading known junctions from GTF file
[2020-03-09 05:49:13] Preparing reads
	 left reads: min. length=75, max. length=75, 31011620 kept reads (19046 discarded)
[2020-03-09 06:00:26] Building transcriptome data files /scratch/3763310.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:00:46] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:08:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:19:19] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:19:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:45:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:48:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:51:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:55:31] Searching for junctions via segment mapping
[2020-03-09 06:59:32] Retrieving sequences for splices
[2020-03-09 07:01:44] Indexing splices
[2020-03-09 07:02:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:02:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:03:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:03:47] Joining segment hits
[2020-03-09 07:07:11] Reporting output tracks
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[2020-03-09 07:31:11] A summary of the alignment counts can be found in /scratch/3763310.1.linga/tophat2/align_summary.txt
[2020-03-09 07:31:11] Run complete: 01:42:09 elapsed