2022-09-09 19:59:25,387 INFO Cutadapt Mode: Paired-end 2022-09-09 19:59:25,387 INFO Cutadapt Input FASTQ [R1]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N32/N32_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz 2022-09-09 19:59:25,387 INFO Cutadapt Input FASTQ [R2]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N32/N32_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz 2022-09-09 19:59:25,387 INFO Cutadapt Output FASTQ [R1]: /tmp/tmpvog0qgap/adapter_R1_0.fastq.gz 2022-09-09 19:59:25,387 INFO Cutadapt Output FASTQ [R2]: /tmp/tmpvog0qgap/adapter_R2_0.fastq.gz 2022-09-09 19:59:25,387 INFO Cutadapt Adapter: illumina 2022-09-09 19:59:25,387 DEBUG SimpleSubprocess cutadapt -j 10 -e 0.2 -m 8 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o "/tmp/tmpvog0qgap/adapter_R1_0.fastq.gz" -p "/tmp/tmpvog0qgap/adapter_R2_0.fastq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N32/N32_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N32/N32_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz" > "/dreamworld/ngs_data/NIPT/N32/N32.InputItem0.cutadapt.txt" 2022-09-09 19:59:29,873 INFO SimpleSubprocess Cutadapt.Trim - 0:00:04 2022-09-09 19:59:29,873 INFO FastQC FastQ: /tmp/tmpvog0qgap/adapter_R1_0.fastq.gz 2022-09-09 19:59:29,873 INFO FastQC Report: /dreamworld/ngs_data/NIPT/N32/N32.InputItem0.fastqc.html 2022-09-09 19:59:29,899 INFO FastQC Subsample: 1000000 2022-09-09 19:59:29,899 DEBUG SimpleSubprocess zcat -q "/tmp/tmpvog0qgap/adapter_R1_0.fastq.gz" | head -4000000 | gzip -c > "/tmp/tmpmf7h3f7d/sample.fastq.gz" 2022-09-09 19:59:36,504 INFO SimpleSubprocess FastQC.Sampling - 0:00:06 2022-09-09 19:59:36,504 DEBUG SimpleSubprocess fastqc -o "/tmp/tmpmf7h3f7d" -t 10 "/tmp/tmpmf7h3f7d/sample.fastq.gz" 2022-09-09 19:59:40,677 INFO SimpleSubprocess FastQC.Analysis - 0:00:04 2022-09-09 19:59:40,677 DEBUG SimpleSubprocess cp "/tmp/tmpmf7h3f7d/sample_fastqc.html" "/dreamworld/ngs_data/NIPT/N32/N32.InputItem0.fastqc.html" 2022-09-09 19:59:40,680 INFO SimpleSubprocess FastQC.Move - 0:00:00 2022-09-09 19:59:40,683 INFO BWA R1: /tmp/tmpvog0qgap/adapter_R1_0.fastq.gz 2022-09-09 19:59:40,683 INFO BWA R2: /tmp/tmpvog0qgap/adapter_R2_0.fastq.gz 2022-09-09 19:59:40,683 INFO BWA Output BAM: /tmp/tmpvog0qgap/temp_0.bam 2022-09-09 19:59:40,683 INFO BWA Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 19:59:40,683 INFO BWA RG Header: @RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.GATCAGAT\tLB:LIB-N32-001\tSM:N32 2022-09-09 19:59:40,683 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; set -o pipefail; bwa mem -R "@RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.GATCAGAT\tLB:LIB-N32-001\tSM:N32" -t 10 -v 1 "/dreamworld/databases/hg19_canonical/hg19_canonical.fa" "/tmp/tmpvog0qgap/adapter_R1_0.fastq.gz" "/tmp/tmpvog0qgap/adapter_R2_0.fastq.gz" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmp6shapftd" -SO queryname -I "/dev/stdin" -O "/tmp/tmpvog0qgap/temp_0.bam" 2022-09-09 20:00:18,417 INFO SimpleSubprocess BWA.AlignAndSort - 0:00:37 2022-09-09 20:00:18,418 DEBUG SimpleSubprocess cp "/tmp/tmpvog0qgap/temp_0.bam" "/dreamworld/ngs_data/NIPT/N32/IRs/N32.primary.bam" 2022-09-09 20:00:18,457 INFO SimpleSubprocess DaemonicPipe.CopyBAM - 0:00:00 2022-09-09 20:00:18,457 DEBUG SimpleSubprocess samtools flagstat -O tsv "/dreamworld/ngs_data/NIPT/N32/IRs/N32.primary.bam" > "/dreamworld/ngs_data/NIPT/N32/N32.primary_stats.txt" 2022-09-09 20:00:18,937 INFO SimpleSubprocess DaemonicPipe.FlagStats - 0:00:00 2022-09-09 20:00:18,950 INFO MarkDuplicates Input: /dreamworld/ngs_data/NIPT/N32/IRs/N32.primary.bam 2022-09-09 20:00:18,950 INFO MarkDuplicates Output: /dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam 2022-09-09 20:00:18,950 INFO MarkDuplicates Metrics: /dreamworld/ngs_data/NIPT/N32/N32.md_metrics.txt 2022-09-09 20:00:18,952 DEBUG SimpleSubprocess source /dreamworld/miniconda3/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/tmpilmy00dd" -M "/dreamworld/ngs_data/NIPT/N32/N32.md_metrics.txt" -I "/dreamworld/ngs_data/NIPT/N32/IRs/N32.primary.bam" -O "/dev/stdout" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmpilmy00dd" -SO coordinate -I "/dev/stdin" -O "/dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam" 2022-09-09 20:00:32,082 INFO SimpleSubprocess MarkDuplicates.RemoveAndSort - 0:00:13 2022-09-09 20:00:32,083 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; gatk BuildBamIndex -I "/dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam" 2022-09-09 20:00:37,418 INFO SimpleSubprocess MarkDuplicates.Index - 0:00:05 2022-09-09 20:00:37,418 INFO CoverageStats BAM File: /dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam 2022-09-09 20:00:37,418 INFO CoverageStats Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 20:00:37,418 INFO CoverageStats Capture BED: /dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed 2022-09-09 20:00:37,419 DEBUG SimpleSubprocess awk 'BEGIN {FS="\t"}; {print $1 FS "0" FS $2}' "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" > "/tmp/tmpq1numh4_/genome.bed" 2022-09-09 20:00:37,422 INFO SimpleSubprocess PrepareGenomeBED.Create - 0:00:00 2022-09-09 20:00:37,422 DEBUG SimpleSubprocess bedtools subtract -a "/tmp/tmpq1numh4_/genome.bed" -b "/dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed" | sed -e 's/$/\t\./' > "/tmp/tmpq1numh4_/not_capture.bed" 2022-09-09 20:00:39,828 INFO SimpleSubprocess CoverageStats.CreateNotCaptureBed - 0:00:02 2022-09-09 20:00:39,828 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" -a "/dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed" -b "/dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpq1numh4_/capture.csv" 2022-09-09 20:00:41,559 INFO SimpleSubprocess CoverageStats.CaptureCoverage - 0:00:01 2022-09-09 20:00:41,559 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" -a "/tmp/tmpq1numh4_/not_capture.bed" -b "/dreamworld/ngs_data/NIPT/N32/IRs/N32.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpq1numh4_/not_capture.csv" 2022-09-09 20:01:01,783 INFO SimpleSubprocess CoverageStats.NotCaptureCoverage - 0:00:20