INFO  08:30:17,464 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:30:17,467 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
INFO  08:30:17,467 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  08:30:17,467 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  08:30:17,467 HelpFormatter - [Thu May 25 08:30:17 UTC 2023] Executing on Linux 5.15.0-69-generic amd64 
INFO  08:30:17,467 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_102-8u102-b14.1-1~bpo8+1-b14 
INFO  08:30:17,471 HelpFormatter - Program Args: -R /home/genomics/rolbrechts/00_Data/00_Reference_genome_C_Canephora/ref_genome_Ccanephora_Denoeud/ref_genome_Ccanephora_WF.fa -T UnifiedGenotyper -I /home/genomics/rolbrechts/sub_bam.list -o /home/genomics/rolbrechts/test_GATK.vcf -L /home/genomics/rolbrechts/00_Data/00_Reference_genome_C_Canephora/ref_genome_Ccanephora_Denoeud/ref_genome_Ccanephora_WF.bed 
INFO  08:30:17,491 HelpFormatter - Executing as root@704c67c431c8 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  08:30:17,491 HelpFormatter - Date/Time: 2023/05/25 08:30:17 
INFO  08:30:17,491 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:30:17,491 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  08:30:17,506 GenomeAnalysisEngine - Strictness is SILENT 
INFO  08:30:17,898 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 
INFO  08:30:17,905 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  08:30:18,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16 
INFO  08:30:18,252 IntervalUtils - Processing 364307609 bp from intervals 
INFO  08:30:18,308 GenomeAnalysisEngine - Preparing for traversal over 10 BAM files 
INFO  08:30:18,403 GenomeAnalysisEngine - Done preparing for traversal 
INFO  08:30:18,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  08:30:18,404 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  08:30:18,404 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  08:30:18,516 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
INFO  08:30:18,517 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values. 
INFO  08:30:48,424 ProgressMeter - Cc_chr2:1016709   3.9209208E7    30.0 s       0.0 s       10.8%     4.6 m       4.1 m 
INFO  08:31:18,426 ProgressMeter - Cc_chr2:51020341   8.914764E7    60.0 s       0.0 s       24.5%     4.1 m       3.1 m 
INFO  08:31:48,428 ProgressMeter - Cc_chr4:22467013   1.47160591E8    90.0 s       0.0 s       40.4%     3.7 m       2.2 m 
INFO  08:32:18,435 ProgressMeter - Cc_chr6:21789189   2.03491087E8   120.0 s       0.0 s       56.0%     3.6 m      94.0 s 
INFO  08:32:48,436 ProgressMeter - Cc_chr8:17565361   2.66653244E8     2.5 m       0.0 s       73.2%     3.4 m      54.0 s 
INFO  08:33:18,437 ProgressMeter - Cc_chr10:23357897   3.26391101E8     3.0 m       0.0 s       89.6%     3.3 m      20.0 s 
INFO  08:33:39,513 ProgressMeter -            done   3.64307609E8     3.4 m       0.0 s      100.0%     3.4 m       0.0 s 
INFO  08:33:39,514 ProgressMeter - Total runtime 201.11 secs, 3.35 min, 0.06 hours 
INFO  08:33:39,514 MicroScheduler - 43431 reads were filtered out during the traversal out of approximately 9532888 total reads (0.46%) 
INFO  08:33:39,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  08:33:39,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadMateFilter 
INFO  08:33:39,514 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter 
INFO  08:33:39,514 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO  08:33:39,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  08:33:39,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO  08:33:39,515 MicroScheduler -   -> 43431 reads (0.46% of total) failing NotPrimaryAlignmentFilter 
INFO  08:33:39,515 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
------------------------------------------------------------------------------------------
Done. ------------------------------------------------------------------------------------------
There were no warn messages.