INFO  08:40:47,801 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:40:47,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
INFO  08:40:47,803 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  08:40:47,803 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  08:40:47,803 HelpFormatter - [Thu May 25 08:40:47 UTC 2023] Executing on Linux 5.15.0-69-generic amd64 
INFO  08:40:47,803 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_102-8u102-b14.1-1~bpo8+1-b14 
INFO  08:40:47,806 HelpFormatter - Program Args: -T SelectVariants -R /home/genomics/rolbrechts/00_Data/00_Reference_genome_C_Canephora/ref_genome_Ccanephora_Denoeud/ref_genome_Ccanephora_WF.fa -V /home/genomics/rolbrechts/test_GATK.vcf --excludeNonVariants -o /home/genomics/rolbrechts/test_GATK.vcf_polymorph.vcf 
INFO  08:40:47,811 HelpFormatter - Executing as root@c1b4ccd03777 on Linux 5.15.0-69-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_102-8u102-b14.1-1~bpo8+1-b14. 
INFO  08:40:47,811 HelpFormatter - Date/Time: 2023/05/25 08:40:47 
INFO  08:40:47,811 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:40:47,812 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:40:47,824 GenomeAnalysisEngine - Strictness is SILENT 
INFO  08:40:47,922 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  08:40:48,045 GenomeAnalysisEngine - Preparing for traversal 
INFO  08:40:48,047 GenomeAnalysisEngine - Done preparing for traversal 
INFO  08:40:48,047 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  08:40:48,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  08:40:48,047 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  08:40:49,790 SelectVariants - 9214 records processed. 
INFO  08:40:49,843 ProgressMeter -            done      9214.0     1.0 s       3.2 m       99.9%     1.0 s       0.0 s 
INFO  08:40:49,843 ProgressMeter - Total runtime 1.80 secs, 0.03 min, 0.00 hours 
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Done. ------------------------------------------------------------------------------------------
There were no warn messages.