[2020-03-09 05:48:26] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:48:26] 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 05:48:28] Reading known junctions from GTF file
[2020-03-09 05:48:30] Preparing reads
	 left reads: min. length=75, max. length=75, 24067329 kept reads (10033 discarded)
[2020-03-09 05:53:18] Building transcriptome data files /scratch/3763317.1.c/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 05:53:27] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 05:57:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:07:40] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:07:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:13:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:13:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:14:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:15:06] Searching for junctions via segment mapping
[2020-03-09 06:18:26] Retrieving sequences for splices
[2020-03-09 06:19:31] Indexing splices
[2020-03-09 06:19:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 06:20:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 06:20:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 06:20:38] Joining segment hits
[2020-03-09 06:22:07] Reporting output tracks
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[2020-03-09 06:44:56] A summary of the alignment counts can be found in /scratch/3763317.1.c/tophat2/align_summary.txt
[2020-03-09 06:44:56] Run complete: 00:56:29 elapsed