[2020-03-09 07:38:12] Beginning TopHat run (v2.1.1)
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[2020-03-09 07:38:12] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 07:38:15] Checking for Bowtie index files (genome)..
[2020-03-09 07:38:15] Checking for reference FASTA file
[2020-03-09 07:38:15] Generating SAM header for Bowtie2Index/genome
[2020-03-09 07:38:19] Reading known junctions from GTF file
[2020-03-09 07:38:23] Preparing reads
	 left reads: min. length=75, max. length=75, 50343089 kept reads (21317 discarded)
[2020-03-09 07:55:21] Building transcriptome data files /scratch/3763324.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 07:55:40] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 08:02:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 08:22:15] Resuming TopHat pipeline with unmapped reads
[2020-03-09 08:22:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 08:46:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 08:49:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 08:52:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 08:54:59] Searching for junctions via segment mapping
[2020-03-09 08:59:46] Retrieving sequences for splices
[2020-03-09 09:01:55] Indexing splices
[2020-03-09 09:02:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 09:03:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 09:03:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 09:04:08] Joining segment hits
[2020-03-09 09:08:26] Reporting output tracks
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[2020-03-09 09:47:28] A summary of the alignment counts can be found in /scratch/3763324.1.linga/tophat2/align_summary.txt
[2020-03-09 09:47:28] Run complete: 02:09:15 elapsed