[2020-03-09 07:03:54] Beginning TopHat run (v2.1.1)
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[2020-03-09 07:03:54] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 07:03:55] Checking for Bowtie index files (genome)..
[2020-03-09 07:03:55] Checking for reference FASTA file
[2020-03-09 07:03:55] Generating SAM header for Bowtie2Index/genome
[2020-03-09 07:03:56] Reading known junctions from GTF file
[2020-03-09 07:03:58] Preparing reads
	 left reads: min. length=75, max. length=75, 12884230 kept reads (5767 discarded)
[2020-03-09 07:06:30] Building transcriptome data files /scratch/3763323.1.c/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 07:06:39] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 07:11:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 07:15:11] Resuming TopHat pipeline with unmapped reads
[2020-03-09 07:15:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 07:18:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 07:19:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 07:19:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 07:19:55] Searching for junctions via segment mapping
[2020-03-09 07:21:47] Retrieving sequences for splices
[2020-03-09 07:22:52] Indexing splices
[2020-03-09 07:23:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:23:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:23:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:23:26] Joining segment hits
[2020-03-09 07:24:47] Reporting output tracks
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[2020-03-09 07:40:30] A summary of the alignment counts can be found in /scratch/3763323.1.c/tophat2/align_summary.txt
[2020-03-09 07:40:30] Run complete: 00:36:36 elapsed