2022-07-29 04:02:58,088 INFO Cutadapt Mode: Paired-end 2022-07-29 04:02:58,089 INFO Cutadapt Input FASTQ [R1]: /Data/NGS_Data/2022-07-25-BGI/Demult/P97_R1.fastq.gz 2022-07-29 04:02:58,089 INFO Cutadapt Input FASTQ [R2]: /Data/NGS_Data/2022-07-25-BGI/Demult/P97_R2.fastq.gz 2022-07-29 04:02:58,089 INFO Cutadapt Output FASTQ [R1]: /tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz 2022-07-29 04:02:58,089 INFO Cutadapt Output FASTQ [R2]: /tmp/tmpqcsu3vpt/adapter_R2_0.fastq.gz 2022-07-29 04:02:58,089 INFO Cutadapt Adapter: illumina 2022-07-29 04:02:58,089 DEBUG SimpleSubprocess cutadapt -j 10 -e 0.2 -m 8 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o "/tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz" -p "/tmp/tmpqcsu3vpt/adapter_R2_0.fastq.gz" "/Data/NGS_Data/2022-07-25-BGI/Demult/P97_R1.fastq.gz" "/Data/NGS_Data/2022-07-25-BGI/Demult/P97_R2.fastq.gz" > "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.InputItem0.cutadapt.txt" 2022-07-29 04:12:51,371 INFO SimpleSubprocess Cutadapt.Trim - 0:09:53 2022-07-29 04:12:51,372 INFO FastQC FastQ: /tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz 2022-07-29 04:12:51,372 INFO FastQC Report: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.InputItem0.fastqc.html 2022-07-29 04:12:51,372 INFO FastQC Subsample: 1000000 2022-07-29 04:12:51,372 DEBUG SimpleSubprocess zcat -q "/tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz" | head -4000000 | gzip -c > "/tmp/tmp1x0jhh87/sample.fastq.gz" 2022-07-29 04:13:27,970 INFO SimpleSubprocess FastQC.Sampling - 0:00:36 2022-07-29 04:13:27,971 DEBUG SimpleSubprocess fastqc -o "/tmp/tmp1x0jhh87" -t 10 "/tmp/tmp1x0jhh87/sample.fastq.gz" 2022-07-29 04:13:44,880 INFO SimpleSubprocess FastQC.Analysis - 0:00:16 2022-07-29 04:13:44,910 DEBUG SimpleSubprocess cp "/tmp/tmp1x0jhh87/sample_fastqc.html" "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.InputItem0.fastqc.html" 2022-07-29 04:13:44,984 INFO SimpleSubprocess FastQC.Move - 0:00:00 2022-07-29 04:13:45,007 INFO BWA R1: /tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz 2022-07-29 04:13:45,007 INFO BWA R2: /tmp/tmpqcsu3vpt/adapter_R2_0.fastq.gz 2022-07-29 04:13:45,007 INFO BWA Output BAM: /tmp/tmpqcsu3vpt/temp_0.bam 2022-07-29 04:13:45,007 INFO BWA Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 04:13:45,007 INFO BWA RG Header: @RG\tID:0\tPL:ILLUMINA\tPU:D-V300114157\tLB:L-001\tSM:S-P97 2022-07-29 04:13:45,065 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-P97" -t 10 -v 1 "/Data/DataBases/hg19_Canonic/hg19.fa" "/tmp/tmpqcsu3vpt/adapter_R1_0.fastq.gz" "/tmp/tmpqcsu3vpt/adapter_R2_0.fastq.gz" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmpnh4pv4j0" -SO queryname -I "/dev/stdin" -O "/tmp/tmpqcsu3vpt/temp_0.bam" 2022-07-29 04:43:07,423 INFO SimpleSubprocess BWA.AlignAndSort - 0:29:22 2022-07-29 04:43:07,489 DEBUG SimpleSubprocess cp "/tmp/tmpqcsu3vpt/temp_0.bam" "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.primary.bam" 2022-07-29 04:43:46,170 INFO SimpleSubprocess DaemonicPipe.CopyBAM - 0:00:38 2022-07-29 04:43:46,170 DEBUG SimpleSubprocess samtools flagstat -O tsv "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.primary.bam" > "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.primary_stats.txt" 2022-07-29 04:45:31,319 INFO SimpleSubprocess DaemonicPipe.FlagStats - 0:01:45 2022-07-29 04:45:34,438 INFO MarkDuplicates Input: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.primary.bam 2022-07-29 04:45:34,439 INFO MarkDuplicates Output: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam 2022-07-29 04:45:34,439 INFO MarkDuplicates Metrics: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.md_metrics.txt 2022-07-29 04:45:34,447 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/tmp65o2zrzw" -M "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.md_metrics.txt" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.primary.bam" -O "/dev/stdout" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmp65o2zrzw" -SO coordinate -I "/dev/stdin" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" 2022-07-29 05:13:48,562 INFO SimpleSubprocess MarkDuplicates.RemoveAndSort - 0:28:14 2022-07-29 05:13:48,563 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" 2022-07-29 05:17:31,749 INFO SimpleSubprocess MarkDuplicates.Index - 0:03:43 2022-07-29 05:17:31,801 INFO CoverageStats BAM File: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam 2022-07-29 05:17:31,802 INFO CoverageStats Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 05:17:31,802 INFO CoverageStats Capture BED: /Data/DataBases/Targets/KAPA_HyperExome_hg19_canonic.bed 2022-07-29 05:17:31,823 DEBUG SimpleSubprocess awk 'BEGIN {FS="\t"}; {print $1 FS "0" FS $2}' "/Data/DataBases/hg19_Canonic/hg19.fa.fai" > "/tmp/tmpmiyuhjzq/genome.bed" 2022-07-29 05:17:31,932 INFO SimpleSubprocess PrepareGenomeBED.Create - 0:00:00 2022-07-29 05:17:31,933 DEBUG SimpleSubprocess bedtools subtract -a "/tmp/tmpmiyuhjzq/genome.bed" -b "/Data/DataBases/Targets/KAPA_HyperExome_hg19_canonic.bed" | sed -e 's/$/\t\./' > "/tmp/tmpmiyuhjzq/not_capture.bed" 2022-07-29 05:17:37,129 INFO SimpleSubprocess CoverageStats.CreateNotCaptureBed - 0:00:05 2022-07-29 05:17:37,145 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/P97/IRs/P97.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpmiyuhjzq/capture.csv" 2022-07-29 05:22:12,852 INFO SimpleSubprocess CoverageStats.CaptureCoverage - 0:04:35 2022-07-29 05:22:12,852 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/Data/DataBases/hg19_Canonic/hg19.fa.fai" -a "/tmp/tmpmiyuhjzq/not_capture.bed" -b "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpmiyuhjzq/not_capture.csv" 2022-07-29 05:28:12,515 INFO SimpleSubprocess CoverageStats.NotCaptureCoverage - 0:05:59 2022-07-29 05:28:14,828 INFO BaseRecalibration Input: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam 2022-07-29 05:28:14,828 INFO BaseRecalibration Output: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.final.bam 2022-07-29 05:28:14,828 INFO BaseRecalibration Known sites: /Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz 2022-07-29 05:28:14,828 INFO BaseRecalibration Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 05:28:14,989 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" 2022-07-29 05:31:58,627 INFO SimpleSubprocess BaseRecalibration.PreIndex - 0:03:43 2022-07-29 05:31:58,694 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/tmpwvyvmifg" -L chr1 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr1.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,694 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/tmpwvyvmifg" -L chr2 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr2.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,694 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/tmpwvyvmifg" -L chr3 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr3.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,694 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/tmpwvyvmifg" -L chr4 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr4.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr5 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr5.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr6 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr6.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr7 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr7.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr8 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr8.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr10 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr10.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:31:58,695 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/tmpwvyvmifg" -L chr9 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr9.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:36:30,949 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr8] - 0:04:32 2022-07-29 05:36:30,949 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/tmpwvyvmifg" -OBI false -L chr8 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr8.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr8.bam" 2022-07-29 05:36:37,099 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr9] - 0:04:38 2022-07-29 05:36:37,099 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/tmpwvyvmifg" -OBI false -L chr9 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr9.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr9.bam" 2022-07-29 05:36:47,884 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr10] - 0:04:49 2022-07-29 05:36:47,884 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/tmpwvyvmifg" -OBI false -L chr10 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr10.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr10.bam" 2022-07-29 05:37:16,495 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr4] - 0:05:17 2022-07-29 05:37:16,495 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/tmpwvyvmifg" -OBI false -L chr4 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr4.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr4.bam" 2022-07-29 05:37:21,458 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr7] - 0:05:22 2022-07-29 05:37:21,459 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/tmpwvyvmifg" -OBI false -L chr7 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr7.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr7.bam" 2022-07-29 05:37:30,150 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr5] - 0:05:31 2022-07-29 05:37:30,150 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/tmpwvyvmifg" -OBI false -L chr5 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr5.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr5.bam" 2022-07-29 05:37:57,329 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr8] - 0:01:26 2022-07-29 05:37:57,330 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/tmpwvyvmifg" -L chr11 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr11.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:38:07,226 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr6] - 0:06:08 2022-07-29 05:38:07,226 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/tmpwvyvmifg" -OBI false -L chr6 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr6.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr6.bam" 2022-07-29 05:38:12,256 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr9] - 0:01:35 2022-07-29 05:38:12,276 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/tmpwvyvmifg" -L chr12 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr12.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:38:25,819 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr10] - 0:01:37 2022-07-29 05:38:25,820 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/tmpwvyvmifg" -L chr13 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr13.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:38:48,589 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr3] - 0:06:49 2022-07-29 05:38:48,590 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/tmpwvyvmifg" -OBI false -L chr3 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr3.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr3.bam" 2022-07-29 05:38:59,518 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr4] - 0:01:43 2022-07-29 05:38:59,542 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/tmpwvyvmifg" -L chr14 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr14.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:39:13,411 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr7] - 0:01:51 2022-07-29 05:39:13,418 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/tmpwvyvmifg" -L chr15 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr15.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:39:27,275 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr5] - 0:01:57 2022-07-29 05:39:27,303 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/tmpwvyvmifg" -L chr16 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr16.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:40:04,837 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr6] - 0:01:57 2022-07-29 05:40:04,869 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/tmpwvyvmifg" -L chr17 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr17.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:40:31,186 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr2] - 0:08:32 2022-07-29 05:40:31,186 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/tmpwvyvmifg" -OBI false -L chr2 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr2.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr2.bam" 2022-07-29 05:40:51,354 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr3] - 0:02:02 2022-07-29 05:40:51,381 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/tmpwvyvmifg" -L chr18 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr18.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:41:10,566 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr13] - 0:02:44 2022-07-29 05:41:10,567 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/tmpwvyvmifg" -OBI false -L chr13 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr13.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr13.bam" 2022-07-29 05:41:19,762 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr1] - 0:09:21 2022-07-29 05:41:19,762 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/tmpwvyvmifg" -OBI false -L chr1 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr1.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr1.bam" 2022-07-29 05:42:01,342 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr13] - 0:00:50 2022-07-29 05:42:01,447 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/tmpwvyvmifg" -L chr19 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr19.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:42:32,572 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr14] - 0:03:33 2022-07-29 05:42:32,613 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/tmpwvyvmifg" -OBI false -L chr14 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr14.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr14.bam" 2022-07-29 05:42:59,820 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr2] - 0:02:28 2022-07-29 05:43:00,629 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/tmpwvyvmifg" -L chr20 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr20.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:43:06,163 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr15] - 0:03:52 2022-07-29 05:43:06,235 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/tmpwvyvmifg" -OBI false -L chr15 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr15.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr15.bam" 2022-07-29 05:43:09,333 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr18] - 0:02:17 2022-07-29 05:43:09,362 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/tmpwvyvmifg" -OBI false -L chr18 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr18.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr18.bam" 2022-07-29 05:43:28,259 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr12] - 0:05:15 2022-07-29 05:43:28,286 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/tmpwvyvmifg" -OBI false -L chr12 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr12.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr12.bam" 2022-07-29 05:43:43,835 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr11] - 0:05:46 2022-07-29 05:43:43,993 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/tmpwvyvmifg" -OBI false -L chr11 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr11.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr11.bam" 2022-07-29 05:43:44,809 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr16] - 0:04:17 2022-07-29 05:43:44,811 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/tmpwvyvmifg" -OBI false -L chr16 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr16.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr16.bam" 2022-07-29 05:43:55,064 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr14] - 0:01:22 2022-07-29 05:43:55,091 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/tmpwvyvmifg" -L chr21 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr21.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:44:03,494 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr18] - 0:00:54 2022-07-29 05:44:03,495 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/tmpwvyvmifg" -L chr22 -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chr22.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:44:15,029 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr1] - 0:02:55 2022-07-29 05:44:15,180 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/tmpwvyvmifg" -L chrX -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chrX.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:44:37,773 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr15] - 0:01:31 2022-07-29 05:44:37,804 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/tmpwvyvmifg" -L chrY -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" --known-sites "/Data/DataBases/dbSNP_BaseRecatibrator/dbsnp151_BaseRecalibrator.vcf.gz" -O "/tmp/tmpwvyvmifg/bqsr_table_chrY.tsv" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:44:54,123 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chrY] - 0:00:16 2022-07-29 05:44:54,123 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/tmpwvyvmifg" -OBI false -L chrY -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chrY.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chrY.bam" 2022-07-29 05:44:55,484 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr17] - 0:04:50 2022-07-29 05:44:55,507 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/tmpwvyvmifg" -OBI false -L chr17 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr17.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr17.bam" 2022-07-29 05:45:07,089 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chrY] - 0:00:12 2022-07-29 05:45:14,840 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr16] - 0:01:30 2022-07-29 05:45:18,624 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr12] - 0:01:50 2022-07-29 05:45:32,035 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr21] - 0:01:36 2022-07-29 05:45:32,058 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/tmpwvyvmifg" -OBI false -L chr21 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr21.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr21.bam" 2022-07-29 05:45:49,560 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr20] - 0:02:48 2022-07-29 05:45:49,560 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/tmpwvyvmifg" -OBI false -L chr20 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr20.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr20.bam" 2022-07-29 05:45:50,610 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr11] - 0:02:06 2022-07-29 05:46:01,458 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr21] - 0:00:29 2022-07-29 05:46:17,300 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr22] - 0:02:13 2022-07-29 05:46:17,300 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/tmpwvyvmifg" -OBI false -L chr22 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr22.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr22.bam" 2022-07-29 05:46:33,690 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr17] - 0:01:38 2022-07-29 05:46:39,165 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr20] - 0:00:49 2022-07-29 05:46:44,851 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chr19] - 0:04:43 2022-07-29 05:46:44,851 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/tmpwvyvmifg" -OBI false -L chr19 -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chr19.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chr19.bam" 2022-07-29 05:47:00,911 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr22] - 0:00:43 2022-07-29 05:47:59,154 INFO SimpleSubprocess ContigBaseRecalibration.MakeTable[chrX] - 0:03:43 2022-07-29 05:47:59,155 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/tmpwvyvmifg" -OBI false -L chrX -bqsr "/tmp/tmpwvyvmifg/bqsr_table_chrX.tsv" -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.dupless.bam" -O "/tmp/tmpwvyvmifg/output_chrX.bam" 2022-07-29 05:48:16,548 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chr19] - 0:01:31 2022-07-29 05:49:40,362 INFO SimpleSubprocess ContigBaseRecalibration.Apply[chrX] - 0:01:41 2022-07-29 05:49:41,252 INFO Threading ContigBaseRecalibration finished on 10 threads, summary time - 0:17:42 2022-07-29 05:49:41,313 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk MergeSamFiles --USE_THREADING true -SO coordinate -I "/tmp/tmpwvyvmifg/output_chr1.bam" -I "/tmp/tmpwvyvmifg/output_chr2.bam" -I "/tmp/tmpwvyvmifg/output_chr3.bam" -I "/tmp/tmpwvyvmifg/output_chr4.bam" -I "/tmp/tmpwvyvmifg/output_chr5.bam" -I "/tmp/tmpwvyvmifg/output_chr6.bam" -I "/tmp/tmpwvyvmifg/output_chr7.bam" -I "/tmp/tmpwvyvmifg/output_chr8.bam" -I "/tmp/tmpwvyvmifg/output_chr9.bam" -I "/tmp/tmpwvyvmifg/output_chr10.bam" -I "/tmp/tmpwvyvmifg/output_chr11.bam" -I "/tmp/tmpwvyvmifg/output_chr12.bam" -I "/tmp/tmpwvyvmifg/output_chr13.bam" -I "/tmp/tmpwvyvmifg/output_chr14.bam" -I "/tmp/tmpwvyvmifg/output_chr15.bam" -I "/tmp/tmpwvyvmifg/output_chr16.bam" -I "/tmp/tmpwvyvmifg/output_chr17.bam" -I "/tmp/tmpwvyvmifg/output_chr18.bam" -I "/tmp/tmpwvyvmifg/output_chr19.bam" -I "/tmp/tmpwvyvmifg/output_chr20.bam" -I "/tmp/tmpwvyvmifg/output_chr21.bam" -I "/tmp/tmpwvyvmifg/output_chr22.bam" -I "/tmp/tmpwvyvmifg/output_chrX.bam" -I "/tmp/tmpwvyvmifg/output_chrY.bam" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.final.bam" 2022-07-29 05:55:55,207 INFO SimpleSubprocess BaseRecalibration.Merge - 0:06:13 2022-07-29 05:55:55,207 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk BuildBamIndex -I "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.final.bam" 2022-07-29 05:59:52,616 INFO SimpleSubprocess BaseRecalibration.PostIndex - 0:03:57 2022-07-29 05:59:54,216 INFO HaplotypeCalling Input BAM: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.final.bam 2022-07-29 05:59:54,216 INFO HaplotypeCalling Output VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf 2022-07-29 05:59:54,216 INFO HaplotypeCalling Reference: /Data/DataBases/hg19_Canonic/hg19.fa 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr1.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr2.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr3.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr4.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr5.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr6.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,518 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr7.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,519 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr8.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,519 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr9.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 05:59:54,519 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr10.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:09:28,250 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr8] - 0:09:33 2022-07-29 06:09:28,282 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr11.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:14:44,651 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr5] - 0:14:50 2022-07-29 06:14:44,672 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr12.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:14:57,241 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr10] - 0:15:02 2022-07-29 06:14:57,285 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr13.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:16:16,695 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr6] - 0:16:22 2022-07-29 06:16:16,722 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr14.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:17:09,837 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr4] - 0:17:15 2022-07-29 06:17:09,838 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr15.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:21:42,715 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr13] - 0:06:45 2022-07-29 06:21:42,716 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr16.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:24:07,286 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr9] - 0:24:12 2022-07-29 06:24:07,309 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr17.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:25:43,034 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr3] - 0:25:48 2022-07-29 06:25:43,059 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr18.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:27:17,872 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr7] - 0:27:23 2022-07-29 06:27:17,892 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr19.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:32:26,933 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr14] - 0:16:10 2022-07-29 06:32:26,934 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr20.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:34:28,096 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr12] - 0:19:43 2022-07-29 06:34:28,097 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr21.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:35:37,372 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr15] - 0:18:27 2022-07-29 06:35:37,373 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chr22.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:36:25,477 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr16] - 0:14:42 2022-07-29 06:36:25,478 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chrX.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:36:38,107 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr18] - 0:10:55 2022-07-29 06:36:38,108 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/P97/P97.final.bam" -O "/tmp/tmpze7zmcgq/output_chrY.vcf" -R "/Data/DataBases/hg19_Canonic/hg19.fa" 2022-07-29 06:38:45,421 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr11] - 0:29:17 2022-07-29 06:38:51,928 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr2] - 0:38:57 2022-07-29 06:38:58,432 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr17] - 0:14:51 2022-07-29 06:42:46,537 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr19] - 0:15:28 2022-07-29 06:42:55,174 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chrY] - 0:06:17 2022-07-29 06:44:28,704 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr20] - 0:12:01 2022-07-29 06:45:47,602 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chrX] - 0:09:22 2022-07-29 06:46:23,394 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr22] - 0:10:46 2022-07-29 06:46:28,006 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr21] - 0:11:59 2022-07-29 06:51:14,768 INFO SimpleSubprocess ContigHaplotypeCalling.Calling[chr1] - 0:51:20 2022-07-29 06:51:14,801 INFO Threading ContigHaplotypeCalling finished on 10 threads, summary time - 0:51:20 2022-07-29 06:51:14,801 DEBUG SimpleSubprocess source /Data/Tools/GATK_conda/bin/activate gatk; gatk MergeVcfs -I "/tmp/tmpze7zmcgq/output_chr1.vcf" -I "/tmp/tmpze7zmcgq/output_chr2.vcf" -I "/tmp/tmpze7zmcgq/output_chr3.vcf" -I "/tmp/tmpze7zmcgq/output_chr4.vcf" -I "/tmp/tmpze7zmcgq/output_chr5.vcf" -I "/tmp/tmpze7zmcgq/output_chr6.vcf" -I "/tmp/tmpze7zmcgq/output_chr7.vcf" -I "/tmp/tmpze7zmcgq/output_chr8.vcf" -I "/tmp/tmpze7zmcgq/output_chr9.vcf" -I "/tmp/tmpze7zmcgq/output_chr10.vcf" -I "/tmp/tmpze7zmcgq/output_chr11.vcf" -I "/tmp/tmpze7zmcgq/output_chr12.vcf" -I "/tmp/tmpze7zmcgq/output_chr13.vcf" -I "/tmp/tmpze7zmcgq/output_chr14.vcf" -I "/tmp/tmpze7zmcgq/output_chr15.vcf" -I "/tmp/tmpze7zmcgq/output_chr16.vcf" -I "/tmp/tmpze7zmcgq/output_chr17.vcf" -I "/tmp/tmpze7zmcgq/output_chr18.vcf" -I "/tmp/tmpze7zmcgq/output_chr19.vcf" -I "/tmp/tmpze7zmcgq/output_chr20.vcf" -I "/tmp/tmpze7zmcgq/output_chr21.vcf" -I "/tmp/tmpze7zmcgq/output_chr22.vcf" -I "/tmp/tmpze7zmcgq/output_chrX.vcf" -I "/tmp/tmpze7zmcgq/output_chrY.vcf" -O "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf" 2022-07-29 06:51:27,474 INFO SimpleSubprocess HaplotypeCalling.Merge - 0:00:12 2022-07-29 06:51:27,514 INFO DaemonicPipe Unit P97 successfully finished, summary time - 2:48:29 2022-07-30 15:26:41,567 INFO ANNOVAR Input VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf 2022-07-30 15:26:41,602 INFO ANNOVAR Output TSV: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.annovar.tsv 2022-07-30 15:26:41,602 INFO ANNOVAR Genome Assembly: hg19 2022-07-30 15:26:41,602 INFO ANNOVAR Databases Dir: /Data/Tools/ANNOVAR_200706/humandb 2022-07-30 15:26:41,602 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 15:26:41,602 DEBUG SimpleSubprocess cp "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf" "/tmp/tmpnw4nziz2/temp.vcf" 2022-07-30 15:26:41,867 INFO SimpleSubprocess ANNOVAR.TempVCF - 0:00:00 2022-07-30 15:26:41,867 DEBUG SimpleSubprocess perl "/Data/Tools/ANNOVAR_200706/table_annovar.pl" "/tmp/tmpnw4nziz2/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 15:47:18,776 WARNING SimpleSubprocess Command 'ANNOVAR.Annotation' has returned ALLOWED non-zero exit code [25] 2022-07-30 15:47:18,777 INFO SimpleSubprocess ANNOVAR.Annotation - 0:20:36 2022-07-30 15:47:18,777 DEBUG SimpleSubprocess cp "/tmp/tmpnw4nziz2/temp.vcf.hg19_multianno.txt" "/Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.annovar.tsv" 2022-07-30 15:47:19,114 INFO SimpleSubprocess ANNOVAR.CopyTSV - 0:00:00 2022-07-30 15:47:19,461 INFO Tsv2Gff3 Name: ENCODE_Blacklist 2022-07-30 15:47:19,461 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/ENCODE_Blacklist 2022-07-30 15:47:19,461 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_0.gff3 2022-07-30 15:47:20,928 INFO Tsv2Gff3 Name: GIAB_AlignProblem 2022-07-30 15:47:20,928 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_AlignProblem 2022-07-30 15:47:20,928 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_1.gff3 2022-07-30 15:47:22,866 INFO Tsv2Gff3 Name: GIAB_AlleleImbalance 2022-07-30 15:47:22,866 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_AlleleImbalance 2022-07-30 15:47:22,867 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_2.gff3 2022-07-30 15:47:25,009 INFO Tsv2Gff3 Name: GIAB_CallConflict 2022-07-30 15:47:25,009 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_CallConflict 2022-07-30 15:47:25,010 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_3.gff3 2022-07-30 15:47:26,523 INFO Tsv2Gff3 Name: GIAB_FilterSSE 2022-07-30 15:47:26,524 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_FilterSSE 2022-07-30 15:47:26,524 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_4.gff3 2022-07-30 15:47:28,025 INFO Tsv2Gff3 Name: GIAB_GenotypeConflict 2022-07-30 15:47:28,025 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_GenotypeConflict 2022-07-30 15:47:28,025 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_5.gff3 2022-07-30 15:47:37,879 INFO Tsv2Gff3 Name: GIAB_QualityIssue 2022-07-30 15:47:37,879 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/GIAB_QualityIssue 2022-07-30 15:47:37,879 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_6.gff3 2022-07-30 15:47:39,647 INFO Tsv2Gff3 Name: NCBI_NGS_DeadZone 2022-07-30 15:47:39,648 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_DeadZone 2022-07-30 15:47:39,648 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_7.gff3 2022-07-30 15:47:41,306 INFO Tsv2Gff3 Name: NCBI_NGS_HighStringency 2022-07-30 15:47:41,307 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_HighStringency 2022-07-30 15:47:41,307 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_8.gff3 2022-07-30 15:47:43,044 INFO Tsv2Gff3 Name: NCBI_NGS_LowStringency 2022-07-30 15:47:43,044 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_NGS_LowStringency 2022-07-30 15:47:43,045 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_9.gff3 2022-07-30 15:47:44,904 INFO Tsv2Gff3 Name: NCBI_Sanger_DeadZone 2022-07-30 15:47:44,904 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/NCBI_Sanger_DeadZone 2022-07-30 15:47:44,904 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_10.gff3 2022-07-30 15:47:46,489 INFO Tsv2Gff3 Name: UCSC_UnusualRegions 2022-07-30 15:47:46,489 INFO Tsv2Gff3 Input TSV db: db/Problematic_Regions/UCSC_UnusualRegions 2022-07-30 15:47:46,489 INFO Tsv2Gff3 Output GFF3: /tmp/tmpgepkqmmu/database_11.gff3 2022-07-30 15:47:46,501 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 15:47:48,006 INFO ANNOVAR Input VCF: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf 2022-07-30 15:47:48,006 INFO ANNOVAR Output TSV: /tmp/tmpgepkqmmu/temp.tsv 2022-07-30 15:47:48,006 INFO ANNOVAR Genome Assembly: hg19 2022-07-30 15:47:48,006 INFO ANNOVAR Databases Dir: /tmp/tmpgepkqmmu 2022-07-30 15:47:48,006 INFO ANNOVAR Databases: GFF3, 12 items [r] 2022-07-30 15:47:48,006 DEBUG SimpleSubprocess cp "/Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.unfiltered.vcf" "/tmp/tmpkf8osqmf/temp.vcf" 2022-07-30 15:47:48,136 INFO SimpleSubprocess ANNOVAR.TempVCF - 0:00:00 2022-07-30 15:47:48,136 DEBUG SimpleSubprocess perl "/Data/Tools/ANNOVAR_200706/table_annovar.pl" "/tmp/tmpkf8osqmf/temp.vcf" "/tmp/tmpgepkqmmu" --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 15:49:04,088 INFO SimpleSubprocess ANNOVAR.Annotation - 0:01:15 2022-07-30 15:49:04,088 DEBUG SimpleSubprocess cp "/tmp/tmpkf8osqmf/temp.vcf.hg19_multianno.txt" "/tmp/tmpgepkqmmu/temp.tsv" 2022-07-30 15:49:04,345 INFO SimpleSubprocess ANNOVAR.CopyTSV - 0:00:00 2022-07-30 15:49:48,637 INFO AnnoFit Input TSV: /Data/NGS_Data/2022-07-25-BGI/Result/P97/IRs/P97.annovar.tsv 2022-07-30 15:49:48,637 INFO AnnoFit Output XLSX: /Data/NGS_Data/2022-07-25-BGI/Result/P97/P97.AnnoFit.xlsx 2022-07-30 15:49:48,637 INFO AnnoFit Chunk Size: 300000 2022-07-30 15:49:50,290 INFO AnnoFit Data loaded - 0:00:01 2022-07-30 15:51:13,670 INFO AnnoFit ANNOVAR table is prepared - 0:01:14 2022-07-30 15:51:15,696 INFO AnnoFit HGMD merged - 0:00:02 2022-07-30 15:52:12,228 INFO AnnoFit XRef merged - 0:00:56 2022-07-30 15:52:23,663 INFO AnnoFit Base filtering is ready - 0:00:11 2022-07-30 15:52:23,664 INFO AnnoFit Chunk #1 - 0:02:24 2022-07-30 15:52:27,836 INFO AnnoFit Filtering is ready - 0:00:02 2022-07-30 15:52:27,873 INFO AnnoFit Genes list is ready - 0:00:00 2022-07-30 15:52:29,432 INFO AnnoFit Hyperlinks are ready - 0:00:01 2022-07-30 15:52:30,549 INFO AnnoFit Files saved - 0:00:01 2022-07-30 15:52:30,549 INFO AnnoFit AnnoFit finish - 0:02:41 2022-07-30 15:52:30,576 INFO AnnoPipe Unit P97 successfully annotated, summary time - 0:25:49