2022-07-29 00:56:26,514 INFO Cutadapt Mode: Paired-end 2022-07-29 00:56:26,514 INFO Cutadapt Input FASTQ [R1]: /Data/NGS_Data/2022-07-25-BGI/Demult/P96_R1.fastq.gz 2022-07-29 00:56:26,514 INFO Cutadapt Input FASTQ [R2]: /Data/NGS_Data/2022-07-25-BGI/Demult/P96_R2.fastq.gz 2022-07-29 00:56:26,514 INFO Cutadapt Output FASTQ [R1]: /tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz 2022-07-29 00:56:26,514 INFO Cutadapt Output FASTQ [R2]: /tmp/tmpr1a5zzp0/adapter_R2_0.fastq.gz 2022-07-29 00:56:26,514 INFO Cutadapt Adapter: illumina 2022-07-29 00:56:26,515 DEBUG SimpleSubprocess cutadapt -j 10 -e 0.2 -m 8 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o "/tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz" -p "/tmp/tmpr1a5zzp0/adapter_R2_0.fastq.gz" "/Data/NGS_Data/2022-07-25-BGI/Demult/P96_R1.fastq.gz" "/Data/NGS_Data/2022-07-25-BGI/Demult/P96_R2.fastq.gz" > "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.InputItem0.cutadapt.txt" 2022-07-29 01:06:53,212 INFO SimpleSubprocess Cutadapt.Trim - 0:10:26 2022-07-29 01:06:53,212 INFO FastQC FastQ: /tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz 2022-07-29 01:06:53,212 INFO FastQC Report: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.InputItem0.fastqc.html 2022-07-29 01:06:53,239 INFO FastQC Subsample: 1000000 2022-07-29 01:06:53,239 DEBUG SimpleSubprocess zcat -q "/tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz" | head -4000000 | gzip -c > "/tmp/tmptl_rr124/sample.fastq.gz" 2022-07-29 01:07:29,590 INFO SimpleSubprocess FastQC.Sampling - 0:00:36 2022-07-29 01:07:29,591 DEBUG SimpleSubprocess fastqc -o "/tmp/tmptl_rr124" -t 10 "/tmp/tmptl_rr124/sample.fastq.gz" 2022-07-29 01:07:46,782 INFO SimpleSubprocess FastQC.Analysis - 0:00:17 2022-07-29 01:07:46,782 DEBUG SimpleSubprocess cp "/tmp/tmptl_rr124/sample_fastqc.html" "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.InputItem0.fastqc.html" 2022-07-29 01:07:46,818 INFO SimpleSubprocess FastQC.Move - 0:00:00 2022-07-29 01:07:46,871 INFO BWA R1: /tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz 2022-07-29 01:07:46,871 INFO BWA R2: /tmp/tmpr1a5zzp0/adapter_R2_0.fastq.gz 2022-07-29 01:07:46,871 INFO BWA Output BAM: /tmp/tmpr1a5zzp0/temp_0.bam 2022-07-29 01:07:46,871 INFO BWA Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 01:07:46,871 INFO BWA RG Header: @RG\tID:0\tPL:ILLUMINA\tPU:D-V300114157\tLB:L-001\tSM:S-P96 2022-07-29 01:07:46,895 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; set -o pipefail; bwa mem -R "@RG\tID:0\tPL:ILLUMINA\tPU:D-V300114157\tLB:L-001\tSM:S-P96" -t 10 -v 1 "/Data/DataBases/hg19_Canonic/hg19.fa" "/tmp/tmpr1a5zzp0/adapter_R1_0.fastq.gz" "/tmp/tmpr1a5zzp0/adapter_R2_0.fastq.gz" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmplhplmt0f" -SO queryname -I "/dev/stdin" -O "/tmp/tmpr1a5zzp0/temp_0.bam" 2022-07-29 01:39:32,227 INFO SimpleSubprocess BWA.AlignAndSort - 0:31:45 2022-07-29 01:39:32,312 DEBUG SimpleSubprocess cp "/tmp/tmpr1a5zzp0/temp_0.bam" "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.primary.bam" 2022-07-29 01:40:28,328 INFO SimpleSubprocess DaemonicPipe.CopyBAM - 0:00:56 2022-07-29 01:40:28,329 DEBUG SimpleSubprocess samtools flagstat -O tsv "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.primary.bam" > "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.primary_stats.txt" 2022-07-29 01:42:21,261 INFO SimpleSubprocess DaemonicPipe.FlagStats - 0:01:52 2022-07-29 01:42:24,657 INFO MarkDuplicates Input: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.primary.bam 2022-07-29 01:42:24,657 INFO MarkDuplicates Output: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam 2022-07-29 01:42:24,657 INFO MarkDuplicates Metrics: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.md_metrics.txt 2022-07-29 01:42:24,707 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; set -o pipefail; gatk --java-options "-XX:+UseParallelGC -XX:ParallelGCThreads=2" MarkDuplicates --REMOVE_DUPLICATES true --VERBOSITY ERROR --ASSUME_SORT_ORDER queryname --TMP_DIR "/tmp/tmpz58d3314" -M "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.md_metrics.txt" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.primary.bam" -O "/dev/stdout" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmpz58d3314" -SO coordinate -I "/dev/stdin" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" 2022-07-29 02:13:09,538 INFO SimpleSubprocess MarkDuplicates.RemoveAndSort - 0:30:44 2022-07-29 02:13:09,538 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" 2022-07-29 02:17:19,229 INFO SimpleSubprocess MarkDuplicates.Index - 0:04:09 2022-07-29 02:17:19,231 INFO CoverageStats BAM File: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam 2022-07-29 02:17:19,231 INFO CoverageStats Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 02:17:19,231 INFO CoverageStats Capture BED: /Data/DataBases/Targets/KAPA_HyperExome_hg19_canonic.bed 2022-07-29 02:17:19,298 DEBUG SimpleSubprocess awk 'BEGIN {FS="\t"}; {print $1 FS "0" FS $2}' "/Data/DataBases/hg19_Canonic/hg19.fa.fai" > "/tmp/tmpxu5qp7ex/genome.bed" 2022-07-29 02:17:19,418 INFO SimpleSubprocess PrepareGenomeBED.Create - 0:00:00 2022-07-29 02:17:19,419 DEBUG SimpleSubprocess bedtools subtract -a "/tmp/tmpxu5qp7ex/genome.bed" -b "/Data/DataBases/Targets/KAPA_HyperExome_hg19_canonic.bed" | sed -e 's/$/\t\./' > "/tmp/tmpxu5qp7ex/not_capture.bed" 2022-07-29 02:17:24,539 INFO SimpleSubprocess CoverageStats.CreateNotCaptureBed - 0:00:05 2022-07-29 02:17:24,561 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/Data/DataBases/hg19_Canonic/hg19.fa.fai" -a "/Data/DataBases/Targets/KAPA_HyperExome_hg19_canonic.bed" -b "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpxu5qp7ex/capture.csv" 2022-07-29 02:22:28,514 INFO SimpleSubprocess CoverageStats.CaptureCoverage - 0:05:03 2022-07-29 02:22:28,515 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/Data/DataBases/hg19_Canonic/hg19.fa.fai" -a "/tmp/tmpxu5qp7ex/not_capture.bed" -b "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpxu5qp7ex/not_capture.csv" 2022-07-29 02:29:02,049 INFO SimpleSubprocess CoverageStats.NotCaptureCoverage - 0:06:33 2022-07-29 02:29:04,649 INFO BaseRecalibration Input: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam 2022-07-29 02:29:04,650 INFO BaseRecalibration Output: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam 2022-07-29 02:29:04,650 INFO BaseRecalibration Known sites: /Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz 2022-07-29 02:29:04,650 INFO BaseRecalibration Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 02:29:04,783 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" 2022-07-29 02:33:11,909 INFO SimpleSubprocess BaseRecalibration.PreIndex - 0:04:07 2022-07-29 02:33:11,952 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr1 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr1.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,952 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr2 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr2.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr3 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr3.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr4 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr4.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr5 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr5.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr6 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr6.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr7 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr7.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr8 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr8.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,954 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr9 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr9.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:33:11,954 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr10 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr10.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:38:07,694 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr8] - 0:04:55 2022-07-29 02:38:07,694 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr8 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr8.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr8.bam" 2022-07-29 02:38:09,589 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr9] - 0:04:57 2022-07-29 02:38:09,590 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr9 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr9.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr9.bam" 2022-07-29 02:38:19,352 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr10] - 0:05:07 2022-07-29 02:38:19,352 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr10 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr10.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr10.bam" 2022-07-29 02:38:42,084 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr4] - 0:05:30 2022-07-29 02:38:42,085 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr4 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr4.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr4.bam" 2022-07-29 02:39:03,247 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr7] - 0:05:51 2022-07-29 02:39:03,247 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr7 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr7.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr7.bam" 2022-07-29 02:39:11,773 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr5] - 0:05:59 2022-07-29 02:39:11,773 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr5 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr5.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr5.bam" 2022-07-29 02:39:22,121 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr6] - 0:06:10 2022-07-29 02:39:22,122 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr6 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr6.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr6.bam" 2022-07-29 02:39:34,191 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr8] - 0:01:26 2022-07-29 02:39:34,191 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr11 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr11.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:40:00,823 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr9] - 0:01:51 2022-07-29 02:40:00,824 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr12 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr12.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:40:08,168 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr10] - 0:01:48 2022-07-29 02:40:08,168 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr13 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr13.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:40:27,346 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr4] - 0:01:45 2022-07-29 02:40:27,375 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr14 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr14.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:40:30,937 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr3] - 0:07:18 2022-07-29 02:40:30,938 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr3 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr3.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr3.bam" 2022-07-29 02:40:58,804 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr7] - 0:01:55 2022-07-29 02:40:58,886 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr15 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr15.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:41:14,244 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr5] - 0:02:02 2022-07-29 02:41:14,263 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr16 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr16.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:41:31,826 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr6] - 0:02:09 2022-07-29 02:41:31,849 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr17 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr17.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:41:46,175 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr2] - 0:08:34 2022-07-29 02:41:46,176 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr2 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr2.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr2.bam" 2022-07-29 02:42:45,848 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr3] - 0:02:14 2022-07-29 02:42:45,866 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr18 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr18.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:42:56,847 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr13] - 0:02:48 2022-07-29 02:42:56,847 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr13 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr13.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr13.bam" 2022-07-29 02:43:12,917 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr1] - 0:10:00 2022-07-29 02:43:12,917 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr1 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr1.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr1.bam" 2022-07-29 02:43:52,952 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr13] - 0:00:56 2022-07-29 02:43:52,953 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr19 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr19.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:44:22,576 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr2] - 0:02:36 2022-07-29 02:44:22,600 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr20 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr20.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:44:27,341 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr14] - 0:03:59 2022-07-29 02:44:27,341 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr14 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr14.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr14.bam" 2022-07-29 02:45:12,078 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr18] - 0:02:26 2022-07-29 02:45:12,079 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr18 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr18.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr18.bam" 2022-07-29 02:45:20,039 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr15] - 0:04:21 2022-07-29 02:45:20,086 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr15 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr15.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr15.bam" 2022-07-29 02:45:44,957 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr12] - 0:05:44 2022-07-29 02:45:44,993 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr12 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr12.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr12.bam" 2022-07-29 02:45:50,998 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr16] - 0:04:36 2022-07-29 02:45:51,038 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr16 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr16.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr16.bam" 2022-07-29 02:45:57,767 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr14] - 0:01:30 2022-07-29 02:45:57,768 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr21 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr21.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:45:59,910 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr11] - 0:06:25 2022-07-29 02:46:00,224 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr11 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr11.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr11.bam" 2022-07-29 02:46:06,205 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr18] - 0:00:54 2022-07-29 02:46:06,205 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chr22 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chr22.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:46:30,253 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr1] - 0:03:17 2022-07-29 02:46:30,979 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chrX -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chrX.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:47:02,249 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr15] - 0:01:42 2022-07-29 02:47:02,253 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G -XX:+UseParallelGC -XX:ParallelGCThreads=2" BaseRecalibrator --gatk-config-file "config/GATK_config.txt" --tmp-dir "/tmp/tmp2pssa_wb" -L chrY -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmp2pssa_wb/bqsr_table_chrY.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 02:47:07,286 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr17] - 0:05:35 2022-07-29 02:47:07,357 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr17 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr17.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr17.bam" 2022-07-29 02:47:24,255 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr20] - 0:03:01 2022-07-29 02:47:24,255 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr20 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr20.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr20.bam" 2022-07-29 02:47:24,778 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chrY] - 0:00:22 2022-07-29 02:47:24,779 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chrY -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chrY.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chrY.bam" 2022-07-29 02:47:37,183 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr21] - 0:01:39 2022-07-29 02:47:37,184 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr21 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr21.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr21.bam" 2022-07-29 02:47:38,839 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr16] - 0:01:47 2022-07-29 02:47:42,669 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chrY] - 0:00:17 2022-07-29 02:47:51,625 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr12] - 0:02:06 2022-07-29 02:48:10,014 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr21] - 0:00:32 2022-07-29 02:48:20,101 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr11] - 0:02:19 2022-07-29 02:48:27,810 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr20] - 0:01:03 2022-07-29 02:48:40,210 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr22] - 0:02:34 2022-07-29 02:48:40,210 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr22 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr22.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr22.bam" 2022-07-29 02:49:05,575 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr17] - 0:01:58 2022-07-29 02:49:05,826 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chrX] - 0:02:34 2022-07-29 02:49:05,826 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chrX -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chrX.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chrX.bam" 2022-07-29 02:49:08,758 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr19] - 0:05:15 2022-07-29 02:49:08,759 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" ApplyBQSR --gatk-config-file "config/GATK_config.txt" -RF MappedReadFilter -RF MappingQualityAvailableReadFilter -RF MappingQualityNotZeroReadFilter -RF NotDuplicateReadFilter -RF NotSecondaryAlignmentReadFilter -RF PassesVendorQualityCheckReadFilter --tmp-dir "/tmp/tmp2pssa_wb" -OBI false -L chr19 -bqsr "/tmp/tmp2pssa_wb/bqsr_table_chr19.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.dupless.bam" -O "/tmp/tmp2pssa_wb/output_chr19.bam" 2022-07-29 02:49:33,243 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr22] - 0:00:53 2022-07-29 02:50:05,678 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chrX] - 0:00:59 2022-07-29 02:50:54,890 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr19] - 0:01:46 2022-07-29 02:50:55,368 INFO Threading ContigBaseRecalibration finished on 10 threads, summary time - 0:17:43 2022-07-29 02:50:55,390 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk MergeSamFiles --USE_THREADING true -SO coordinate -I "/tmp/tmp2pssa_wb/output_chr1.bam" -I "/tmp/tmp2pssa_wb/output_chr2.bam" -I "/tmp/tmp2pssa_wb/output_chr3.bam" -I "/tmp/tmp2pssa_wb/output_chr4.bam" -I "/tmp/tmp2pssa_wb/output_chr5.bam" -I "/tmp/tmp2pssa_wb/output_chr6.bam" -I "/tmp/tmp2pssa_wb/output_chr7.bam" -I "/tmp/tmp2pssa_wb/output_chr8.bam" -I "/tmp/tmp2pssa_wb/output_chr9.bam" -I "/tmp/tmp2pssa_wb/output_chr10.bam" -I "/tmp/tmp2pssa_wb/output_chr11.bam" -I "/tmp/tmp2pssa_wb/output_chr12.bam" -I "/tmp/tmp2pssa_wb/output_chr13.bam" -I "/tmp/tmp2pssa_wb/output_chr14.bam" -I "/tmp/tmp2pssa_wb/output_chr15.bam" -I "/tmp/tmp2pssa_wb/output_chr16.bam" -I "/tmp/tmp2pssa_wb/output_chr17.bam" -I "/tmp/tmp2pssa_wb/output_chr18.bam" -I "/tmp/tmp2pssa_wb/output_chr19.bam" -I "/tmp/tmp2pssa_wb/output_chr20.bam" -I "/tmp/tmp2pssa_wb/output_chr21.bam" -I "/tmp/tmp2pssa_wb/output_chr22.bam" -I "/tmp/tmp2pssa_wb/output_chrX.bam" -I "/tmp/tmp2pssa_wb/output_chrY.bam" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" 2022-07-29 02:58:09,265 INFO SimpleSubprocess BaseRecalibration.Merge - 0:07:13 2022-07-29 02:58:09,267 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" 2022-07-29 03:02:35,789 INFO SimpleSubprocess BaseRecalibration.PostIndex - 0:04:26 2022-07-29 03:02:37,766 INFO HaplotypeCalling Input BAM: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam 2022-07-29 03:02:37,766 INFO HaplotypeCalling Output VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf 2022-07-29 03:02:37,766 INFO HaplotypeCalling Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 03:02:38,142 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr1 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr1.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,142 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr2 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr2.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,142 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr3 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr3.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,179 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr4 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr4.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,179 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr5 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr5.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,179 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr6 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr6.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,179 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr7 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr7.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,180 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr8 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr8.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,180 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr9 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr9.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:02:38,180 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr10 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr10.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:13:01,246 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr8] - 0:10:23 2022-07-29 03:13:01,275 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr11 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr11.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:17:55,692 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr4] - 0:15:17 2022-07-29 03:17:55,693 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr12 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr12.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:18:10,056 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr5] - 0:15:31 2022-07-29 03:18:10,057 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr13 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr13.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:18:59,539 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr10] - 0:16:21 2022-07-29 03:18:59,540 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr14 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr14.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:25:45,577 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr3] - 0:23:07 2022-07-29 03:25:45,605 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr15 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr15.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:26:33,961 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr13] - 0:08:23 2022-07-29 03:26:33,962 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr16 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr16.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:26:34,676 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr9] - 0:23:56 2022-07-29 03:26:34,701 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr17 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr17.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:28:25,444 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr6] - 0:25:47 2022-07-29 03:28:25,477 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr18 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr18.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:33:23,575 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr7] - 0:30:45 2022-07-29 03:33:23,598 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr19 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr19.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:35:00,877 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr12] - 0:17:05 2022-07-29 03:35:00,877 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr20 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr20.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:36:32,871 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr18] - 0:08:07 2022-07-29 03:36:32,872 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr21 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr21.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:37:13,360 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr14] - 0:18:13 2022-07-29 03:37:13,361 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chr22 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chr22.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:38:49,773 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr11] - 0:25:48 2022-07-29 03:38:49,774 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chrX -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chrX.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:43:40,610 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr17] - 0:17:05 2022-07-29 03:43:40,611 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk --java-options "-Xmx3G" HaplotypeCaller --native-pair-hmm-threads 2 -OVI false --dont-use-soft-clipped-bases true -L chrY -I "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.final.bam" -O "/tmp/tmp2gbleo__/output_chrY.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 03:44:21,561 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chrX] - 0:05:31 2022-07-29 03:44:33,616 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr15] - 0:18:48 2022-07-29 03:44:41,816 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr16] - 0:18:07 2022-07-29 03:46:41,201 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr22] - 0:09:27 2022-07-29 03:47:01,349 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr20] - 0:12:00 2022-07-29 03:47:19,422 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr21] - 0:10:46 2022-07-29 03:49:27,208 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chrY] - 0:05:46 2022-07-29 03:49:45,648 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr2] - 0:47:07 2022-07-29 03:51:05,102 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr19] - 0:17:41 2022-07-29 04:02:44,966 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr1] - 1:00:06 2022-07-29 04:02:45,012 INFO Threading ContigHaplotypeCalling finished on 10 threads, summary time - 1:00:06 2022-07-29 04:02:45,013 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk MergeVcfs -I "/tmp/tmp2gbleo__/output_chr1.vcf" -I "/tmp/tmp2gbleo__/output_chr2.vcf" -I "/tmp/tmp2gbleo__/output_chr3.vcf" -I "/tmp/tmp2gbleo__/output_chr4.vcf" -I "/tmp/tmp2gbleo__/output_chr5.vcf" -I "/tmp/tmp2gbleo__/output_chr6.vcf" -I "/tmp/tmp2gbleo__/output_chr7.vcf" -I "/tmp/tmp2gbleo__/output_chr8.vcf" -I "/tmp/tmp2gbleo__/output_chr9.vcf" -I "/tmp/tmp2gbleo__/output_chr10.vcf" -I "/tmp/tmp2gbleo__/output_chr11.vcf" -I "/tmp/tmp2gbleo__/output_chr12.vcf" -I "/tmp/tmp2gbleo__/output_chr13.vcf" -I "/tmp/tmp2gbleo__/output_chr14.vcf" -I "/tmp/tmp2gbleo__/output_chr15.vcf" -I "/tmp/tmp2gbleo__/output_chr16.vcf" -I "/tmp/tmp2gbleo__/output_chr17.vcf" -I "/tmp/tmp2gbleo__/output_chr18.vcf" -I "/tmp/tmp2gbleo__/output_chr19.vcf" -I "/tmp/tmp2gbleo__/output_chr20.vcf" -I "/tmp/tmp2gbleo__/output_chr21.vcf" -I "/tmp/tmp2gbleo__/output_chr22.vcf" -I "/tmp/tmp2gbleo__/output_chrX.vcf" -I "/tmp/tmp2gbleo__/output_chrY.vcf" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf" 2022-07-29 04:02:57,918 INFO SimpleSubprocess HaplotypeCalling.Merge - 0:00:12 2022-07-29 04:02:57,955 INFO DaemonicPipe Unit P96 successfully finished, summary time - 3:06:31 2022-07-30 15:00:28,582 INFO ANNOVAR Input VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf 2022-07-30 15:00:28,606 INFO ANNOVAR Output TSV: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.annovar.tsv 2022-07-30 15:00:28,606 INFO ANNOVAR Genome Assembly: hg19 2022-07-30 15:00:28,606 INFO ANNOVAR Databases Dir: /Data/Tools/ANNOVAR_200706/humandb 2022-07-30 15:00:28,607 INFO ANNOVAR Databases: refGene[g]; knownGene[g]; ensGene[g]; dbnsfp35c[f]; dbscsnv11[f]; intervar_20180118[f]; gnomad211_genome[f]; gene4denovo201907[f]; kaviar_20150923[f]; hrcr1[f]; abraom[f]; ALL.sites.2015_08[f]; AFR.sites.2015_08[f]; AMR.sites.2015_08[f]; EUR.sites.2015_08[f]; EAS.sites.2015_08[f]; SAS.sites.2015_08[f]; gme[f]; esp6500siv2_all[f]; avsnp150[f]; clinvar_20200316[f]; regsnpintron[f]; revel[f]; gwava[f] 2022-07-30 15:00:28,607 DEBUG SimpleSubprocess cp "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf" "/tmp/tmprno8atse/temp.vcf" 2022-07-30 15:00:28,966 INFO SimpleSubprocess ANNOVAR.TempVCF - 0:00:00 2022-07-30 15:00:28,967 DEBUG SimpleSubprocess perl "/Data/Tools/ANNOVAR_200706/table_annovar.pl" "/tmp/tmprno8atse/temp.vcf" "/Data/Tools/ANNOVAR_200706/humandb" --buildver hg19 --protocol refGene,knownGene,ensGene,dbnsfp35c,dbscsnv11,intervar_20180118,gnomad211_genome,gene4denovo201907,kaviar_20150923,hrcr1,abraom,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EUR.sites.2015_08,EAS.sites.2015_08,SAS.sites.2015_08,gme,esp6500siv2_all,avsnp150,clinvar_20200316,regsnpintron,revel,gwava --operation g,g,g,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f --gff3dbfile --remove --vcfinput --thread 10 2022-07-30 15:21:21,365 WARNING SimpleSubprocess Command 'ANNOVAR.Annotation' has returned ALLOWED non-zero exit code [25] 2022-07-30 15:21:21,365 INFO SimpleSubprocess ANNOVAR.Annotation - 0:20:52 2022-07-30 15:21:21,366 DEBUG SimpleSubprocess cp "/tmp/tmprno8atse/temp.vcf.hg19_multianno.txt" "/Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.annovar.tsv" 2022-07-30 15:21:21,692 INFO SimpleSubprocess ANNOVAR.CopyTSV - 0:00:00 2022-07-30 15:21:22,056 INFO Tsv2Gff3 Name: ENCODE_Blacklist 2022-07-30 15:21:22,056 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/ENCODE_Blacklist 2022-07-30 15:21:22,056 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_0.gff3 2022-07-30 15:21:23,480 INFO Tsv2Gff3 Name: GIAB_AlignProblem 2022-07-30 15:21:23,481 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_AlignProblem 2022-07-30 15:21:23,481 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_1.gff3 2022-07-30 15:21:25,427 INFO Tsv2Gff3 Name: GIAB_AlleleImbalance 2022-07-30 15:21:25,427 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_AlleleImbalance 2022-07-30 15:21:25,427 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_2.gff3 2022-07-30 15:21:27,571 INFO Tsv2Gff3 Name: GIAB_CallConflict 2022-07-30 15:21:27,571 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_CallConflict 2022-07-30 15:21:27,571 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_3.gff3 2022-07-30 15:21:29,087 INFO Tsv2Gff3 Name: GIAB_FilterSSE 2022-07-30 15:21:29,087 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_FilterSSE 2022-07-30 15:21:29,087 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_4.gff3 2022-07-30 15:21:30,624 INFO Tsv2Gff3 Name: GIAB_GenotypeConflict 2022-07-30 15:21:30,624 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_GenotypeConflict 2022-07-30 15:21:30,624 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_5.gff3 2022-07-30 15:21:40,967 INFO Tsv2Gff3 Name: GIAB_QualityIssue 2022-07-30 15:21:40,967 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_QualityIssue 2022-07-30 15:21:40,967 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_6.gff3 2022-07-30 15:21:42,689 INFO Tsv2Gff3 Name: NCBI_NGS_DeadZone 2022-07-30 15:21:42,689 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_DeadZone 2022-07-30 15:21:42,710 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_7.gff3 2022-07-30 15:21:44,281 INFO Tsv2Gff3 Name: NCBI_NGS_HighStringency 2022-07-30 15:21:44,281 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_HighStringency 2022-07-30 15:21:44,281 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_8.gff3 2022-07-30 15:21:45,988 INFO Tsv2Gff3 Name: NCBI_NGS_LowStringency 2022-07-30 15:21:45,988 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_LowStringency 2022-07-30 15:21:45,988 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_9.gff3 2022-07-30 15:21:47,811 INFO Tsv2Gff3 Name: NCBI_Sanger_DeadZone 2022-07-30 15:21:47,811 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_Sanger_DeadZone 2022-07-30 15:21:47,812 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_10.gff3 2022-07-30 15:21:49,333 INFO Tsv2Gff3 Name: UCSC_UnusualRegions 2022-07-30 15:21:49,333 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/UCSC_UnusualRegions 2022-07-30 15:21:49,333 INFO Tsv2Gff3 Output GFF3: /tmp/tmp2yvjb04k/database_11.gff3 2022-07-30 15:21:49,362 WARNING Tsv2Gff3 Contigs will be removed from database "UCSC_UnusualRegions": chr10_gl383543_fix, chr10_gl383544_fix, chr10_gl383545_alt, chr10_gl383546_alt, chr10_gl877873_fix, chr10_jh591181_fix, chr10_jh591182_fix, chr10_jh591183_fix, chr10_jh636060_fix, chr10_jh806580_fix, chr10_kb663606_fix, chr10_ke332501_fix, chr11_gl000202_random, chr11_gl383547_alt, chr11_gl582973_fix, chr11_gl949744_fix, chr11_jh159136_alt, chr11_jh159137_alt, chr11_jh159138_fix, chr11_jh159139_fix, chr11_jh159140_fix, chr11_jh159141_fix, chr11_jh159142_fix, chr11_jh159143_fix, chr11_jh591184_fix, chr11_jh591185_fix, chr11_jh720443_fix, chr11_jh806581_fix, chr12_gl383548_fix, chr12_gl383549_alt, chr12_gl383550_alt, chr12_gl383551_alt, chr12_gl383552_alt, chr12_gl383553_alt, chr12_gl582974_fix, chr12_gl877875_alt, chr12_gl877876_alt, chr12_gl949745_alt, chr12_jh720444_fix, chr12_kb663607_fix, chr13_gl582975_fix, chr14_kb021645_fix, chr15_gl383554_alt, chr15_gl383555_alt, chr15_jh720445_fix, chr16_gl383556_alt, chr16_gl383557_alt, chr16_jh720446_fix, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr17_gl383558_fix, chr17_gl383559_fix, chr17_gl383560_fix, chr17_gl383561_fix, chr17_gl383562_fix, chr17_gl383563_alt, chr17_gl383564_alt, chr17_gl383565_alt, chr17_gl383566_alt, chr17_gl582976_fix, chr17_jh159144_fix, chr17_jh159145_fix, chr17_jh159146_alt, chr17_jh159147_alt, chr17_jh159148_alt, chr17_jh591186_fix, chr17_jh636061_fix, chr17_jh720447_fix, chr17_jh806582_fix, chr17_kb021646_fix, chr17_ke332502_fix, chr18_gl000207_random, chr18_gl383567_alt, chr18_gl383568_alt, chr18_gl383569_alt, chr18_gl383570_alt, chr18_gl383571_alt, chr18_gl383572_alt, chr19_gl000208_random, chr19_gl000209_random, chr19_gl383573_alt, chr19_gl383574_alt, chr19_gl383575_alt, chr19_gl383576_alt, chr19_gl582977_fix, chr19_gl949746_alt, chr19_gl949747_alt, chr19_gl949748_alt, chr19_gl949749_alt, chr19_gl949750_alt, chr19_gl949751_alt, chr19_gl949752_alt, chr19_gl949753_alt, chr19_jh159149_fix, chr19_kb021647_fix, chr19_ke332505_fix, chr1_gl000191_random, chr1_gl000192_random, chr1_gl383516_fix, chr1_gl383517_fix, chr1_gl383518_alt, chr1_gl383519_alt, chr1_gl383520_alt, chr1_gl949741_fix, chr1_jh636052_fix, chr1_jh636053_fix, chr1_jh636054_fix, chr1_jh806573_fix, chr1_jh806574_fix, chr1_jh806575_fix, chr20_gl383577_alt, chr20_gl582979_fix, chr20_jh720448_fix, chr20_kb663608_fix, chr21_gl000210_random, chr21_gl383578_alt, chr21_gl383579_alt, chr21_gl383580_alt, chr21_gl383581_alt, chr21_ke332506_fix, chr22_gl383582_alt, chr22_gl383583_alt, chr22_jh720449_fix, chr22_jh806583_fix, chr22_jh806584_fix, chr22_jh806585_fix, chr22_jh806586_fix, chr22_kb663609_alt, chr2_gl383521_alt, chr2_gl383522_alt, chr2_gl582966_alt, chr2_gl877870_fix, chr2_gl877871_fix, chr2_kb663603_fix, chr3_gl383523_fix, chr3_gl383524_fix, chr3_gl383525_fix, chr3_gl383526_alt, chr3_jh159131_fix, chr3_jh159132_fix, chr3_jh636055_alt, chr3_ke332495_fix, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr4_gl383527_alt, chr4_gl383528_alt, chr4_gl383529_alt, chr4_gl582967_fix, chr4_gl877872_fix, chr4_ke332496_fix, chr5_gl339449_alt, chr5_gl383530_alt, chr5_gl383531_alt, chr5_gl383532_alt, chr5_gl949742_alt, chr5_jh159133_fix, chr5_ke332497_fix, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_gl383533_alt, chr6_jh636056_fix, chr6_jh636057_fix, chr6_jh806576_fix, chr6_kb021644_alt, chr6_kb663604_fix, chr6_ke332498_fix, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr7_gl383534_alt, chr7_gl582968_fix, chr7_gl582969_fix, chr7_gl582970_fix, chr7_gl582971_fix, chr7_gl582972_fix, chr7_jh159134_fix, chr7_jh636058_fix, chr7_ke332499_fix, chr8_gl000196_random, chr8_gl000197_random, chr8_gl383535_fix, chr8_gl383536_fix, chr8_gl949743_fix, chr8_jh159135_fix, chr8_ke332500_fix, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr9_gl339450_fix, chr9_gl383537_fix, chr9_gl383538_fix, chr9_gl383539_alt, chr9_gl383540_alt, chr9_gl383541_alt, chr9_gl383542_alt, chr9_jh636059_fix, chr9_jh806577_fix, chr9_jh806578_fix, chr9_jh806579_fix, chr9_kb663605_fix, chrM, chrMT, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249, chrX_gl877877_fix, chrX_jh159150_fix, chrX_jh720451_fix, chrX_jh720452_fix, chrX_jh720453_fix, chrX_jh720454_fix, chrX_jh720455_fix, chrX_jh806587_fix, chrX_jh806588_fix, chrX_jh806589_fix, chrX_jh806590_fix, chrX_jh806591_fix, chrX_jh806592_fix, chrX_jh806593_fix, chrX_jh806594_fix, chrX_jh806595_fix, chrX_jh806596_fix, chrX_jh806597_fix, chrX_jh806598_fix, chrX_jh806599_fix, chrX_jh806600_fix, chrX_jh806601_fix, chrX_jh806602_fix, chrX_jh806603_fix, chrX_kb021648_fix 2022-07-30 15:21:50,799 INFO ANNOVAR Input VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf 2022-07-30 15:21:50,799 INFO ANNOVAR Output TSV: /tmp/tmp2yvjb04k/temp.tsv 2022-07-30 15:21:50,799 INFO ANNOVAR Genome Assembly: hg19 2022-07-30 15:21:50,799 INFO ANNOVAR Databases Dir: /tmp/tmp2yvjb04k 2022-07-30 15:21:50,799 INFO ANNOVAR Databases: GFF3, 12 items [r] 2022-07-30 15:21:50,800 DEBUG SimpleSubprocess cp "/Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.unfiltered.vcf" "/tmp/tmpvwc2wlxl/temp.vcf" 2022-07-30 15:21:50,931 INFO SimpleSubprocess ANNOVAR.TempVCF - 0:00:00 2022-07-30 15:21:50,932 DEBUG SimpleSubprocess perl "/Data/Tools/ANNOVAR_200706/table_annovar.pl" "/tmp/tmpvwc2wlxl/temp.vcf" "/tmp/tmp2yvjb04k" --buildver hg19 --protocol gff3,gff3,gff3,gff3,gff3,gff3,gff3,gff3,gff3,gff3,gff3,gff3 --operation r,r,r,r,r,r,r,r,r,r,r,r --gff3dbfile database_0.gff3,database_1.gff3,database_2.gff3,database_3.gff3,database_4.gff3,database_5.gff3,database_6.gff3,database_7.gff3,database_8.gff3,database_9.gff3,database_10.gff3,database_11.gff3 --remove --vcfinput --thread 10 2022-07-30 15:23:09,756 INFO SimpleSubprocess ANNOVAR.Annotation - 0:01:18 2022-07-30 15:23:09,756 DEBUG SimpleSubprocess cp "/tmp/tmpvwc2wlxl/temp.vcf.hg19_multianno.txt" "/tmp/tmp2yvjb04k/temp.tsv" 2022-07-30 15:23:09,957 INFO SimpleSubprocess ANNOVAR.CopyTSV - 0:00:00 2022-07-30 15:23:56,341 INFO AnnoFit Input TSV: /Data/NGS_Data/2022-07-25-BGI/Result/P96/IRs/P96.annovar.tsv 2022-07-30 15:23:56,341 INFO AnnoFit Output XLSX: /Data/NGS_Data/2022-07-25-BGI/Result/P96/P96.AnnoFit.xlsx 2022-07-30 15:23:56,341 INFO AnnoFit Chunk Size: 300000 2022-07-30 15:23:58,004 INFO AnnoFit Data loaded - 0:00:01 2022-07-30 15:25:22,744 INFO AnnoFit ANNOVAR table is prepared - 0:01:15 2022-07-30 15:25:24,836 INFO AnnoFit HGMD merged - 0:00:02 2022-07-30 15:26:22,987 INFO AnnoFit XRef merged - 0:00:58 2022-07-30 15:26:34,397 INFO AnnoFit Base filtering is ready - 0:00:11 2022-07-30 15:26:34,398 INFO AnnoFit Chunk #1 - 0:02:26 2022-07-30 15:26:38,630 INFO AnnoFit Filtering is ready - 0:00:02 2022-07-30 15:26:38,668 INFO AnnoFit Genes list is ready - 0:00:00 2022-07-30 15:26:40,153 INFO AnnoFit Hyperlinks are ready - 0:00:01 2022-07-30 15:26:41,531 INFO AnnoFit Files saved - 0:00:01 2022-07-30 15:26:41,531 INFO AnnoFit AnnoFit finish - 0:02:45 2022-07-30 15:26:41,566 INFO AnnoPipe Unit P96 successfully annotated, summary time - 0:26:12