2022-09-09 20:24:11,338 INFO Cutadapt Mode: Paired-end 2022-09-09 20:24:11,338 INFO Cutadapt Input FASTQ [R1]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N40/N40_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz 2022-09-09 20:24:11,338 INFO Cutadapt Input FASTQ [R2]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N40/N40_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz 2022-09-09 20:24:11,338 INFO Cutadapt Output FASTQ [R1]: /tmp/tmp67b0p92w/adapter_R1_0.fastq.gz 2022-09-09 20:24:11,338 INFO Cutadapt Output FASTQ [R2]: /tmp/tmp67b0p92w/adapter_R2_0.fastq.gz 2022-09-09 20:24:11,338 INFO Cutadapt Adapter: illumina 2022-09-09 20:24:11,338 DEBUG SimpleSubprocess cutadapt -j 10 -e 0.2 -m 8 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o "/tmp/tmp67b0p92w/adapter_R1_0.fastq.gz" -p "/tmp/tmp67b0p92w/adapter_R2_0.fastq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N40/N40_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N40/N40_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz" > "/dreamworld/ngs_data/NIPT/N40/N40.InputItem0.cutadapt.txt" 2022-09-09 20:24:18,438 INFO SimpleSubprocess Cutadapt.Trim - 0:00:07 2022-09-09 20:24:18,439 INFO FastQC FastQ: /tmp/tmp67b0p92w/adapter_R1_0.fastq.gz 2022-09-09 20:24:18,439 INFO FastQC Report: /dreamworld/ngs_data/NIPT/N40/N40.InputItem0.fastqc.html 2022-09-09 20:24:18,439 INFO FastQC Subsample: 1000000 2022-09-09 20:24:18,439 DEBUG SimpleSubprocess zcat -q "/tmp/tmp67b0p92w/adapter_R1_0.fastq.gz" | head -4000000 | gzip -c > "/tmp/tmp16g61xtk/sample.fastq.gz" 2022-09-09 20:24:28,209 INFO SimpleSubprocess FastQC.Sampling - 0:00:09 2022-09-09 20:24:28,209 DEBUG SimpleSubprocess fastqc -o "/tmp/tmp16g61xtk" -t 10 "/tmp/tmp16g61xtk/sample.fastq.gz" 2022-09-09 20:24:33,377 INFO SimpleSubprocess FastQC.Analysis - 0:00:05 2022-09-09 20:24:33,377 DEBUG SimpleSubprocess cp "/tmp/tmp16g61xtk/sample_fastqc.html" "/dreamworld/ngs_data/NIPT/N40/N40.InputItem0.fastqc.html" 2022-09-09 20:24:33,380 INFO SimpleSubprocess FastQC.Move - 0:00:00 2022-09-09 20:24:33,428 INFO BWA R1: /tmp/tmp67b0p92w/adapter_R1_0.fastq.gz 2022-09-09 20:24:33,428 INFO BWA R2: /tmp/tmp67b0p92w/adapter_R2_0.fastq.gz 2022-09-09 20:24:33,428 INFO BWA Output BAM: /tmp/tmp67b0p92w/temp_0.bam 2022-09-09 20:24:33,428 INFO BWA Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 20:24:33,429 INFO BWA RG Header: @RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.TAGCTTAT\tLB:LIB-N40-003\tSM:N40 2022-09-09 20:24:33,429 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; set -o pipefail; bwa mem -R "@RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.TAGCTTAT\tLB:LIB-N40-003\tSM:N40" -t 10 -v 1 "/dreamworld/databases/hg19_canonical/hg19_canonical.fa" "/tmp/tmp67b0p92w/adapter_R1_0.fastq.gz" "/tmp/tmp67b0p92w/adapter_R2_0.fastq.gz" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmp5yysu4gu" -SO queryname -I "/dev/stdin" -O "/tmp/tmp67b0p92w/temp_0.bam" 2022-09-09 20:25:29,162 INFO SimpleSubprocess BWA.AlignAndSort - 0:00:55 2022-09-09 20:25:29,162 DEBUG SimpleSubprocess cp "/tmp/tmp67b0p92w/temp_0.bam" "/dreamworld/ngs_data/NIPT/N40/IRs/N40.primary.bam" 2022-09-09 20:25:29,222 INFO SimpleSubprocess DaemonicPipe.CopyBAM - 0:00:00 2022-09-09 20:25:29,222 DEBUG SimpleSubprocess samtools flagstat -O tsv "/dreamworld/ngs_data/NIPT/N40/IRs/N40.primary.bam" > "/dreamworld/ngs_data/NIPT/N40/N40.primary_stats.txt" 2022-09-09 20:25:29,971 INFO SimpleSubprocess DaemonicPipe.FlagStats - 0:00:00 2022-09-09 20:25:29,992 INFO MarkDuplicates Input: /dreamworld/ngs_data/NIPT/N40/IRs/N40.primary.bam 2022-09-09 20:25:29,992 INFO MarkDuplicates Output: /dreamworld/ngs_data/NIPT/N40/IRs/N40.dupless.bam 2022-09-09 20:25:29,992 INFO MarkDuplicates Metrics: /dreamworld/ngs_data/NIPT/N40/N40.md_metrics.txt 2022-09-09 20:25:30,007 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/tmpchr7qe_l" -M "/dreamworld/ngs_data/NIPT/N40/N40.md_metrics.txt" -I "/dreamworld/ngs_data/NIPT/N40/IRs/N40.primary.bam" -O "/dev/stdout" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmpchr7qe_l" -SO coordinate -I "/dev/stdin" -O "/dreamworld/ngs_data/NIPT/N40/IRs/N40.dupless.bam" 2022-09-09 20:25:46,845 INFO SimpleSubprocess MarkDuplicates.RemoveAndSort - 0:00:16 2022-09-09 20:25:46,845 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; gatk BuildBamIndex -I "/dreamworld/ngs_data/NIPT/N40/IRs/N40.dupless.bam" 2022-09-09 20:25:53,030 INFO SimpleSubprocess MarkDuplicates.Index - 0:00:06 2022-09-09 20:25:53,030 INFO CoverageStats BAM File: /dreamworld/ngs_data/NIPT/N40/IRs/N40.dupless.bam 2022-09-09 20:25:53,030 INFO CoverageStats Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 20:25:53,030 INFO CoverageStats Capture BED: /dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed 2022-09-09 20:25:53,030 DEBUG SimpleSubprocess awk 'BEGIN {FS="\t"}; {print $1 FS "0" FS $2}' "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" > "/tmp/tmpivovkxoj/genome.bed" 2022-09-09 20:25:53,033 INFO SimpleSubprocess PrepareGenomeBED.Create - 0:00:00 2022-09-09 20:25:53,033 DEBUG SimpleSubprocess bedtools subtract -a "/tmp/tmpivovkxoj/genome.bed" -b "/dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed" | sed -e 's/$/\t\./' > "/tmp/tmpivovkxoj/not_capture.bed" 2022-09-09 20:25:55,438 INFO SimpleSubprocess CoverageStats.CreateNotCaptureBed - 0:00:02 2022-09-09 20:25:55,438 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/N40/IRs/N40.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpivovkxoj/capture.csv" 2022-09-09 20:25:57,808 INFO SimpleSubprocess CoverageStats.CaptureCoverage - 0:00:02 2022-09-09 20:25:57,808 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" -a "/tmp/tmpivovkxoj/not_capture.bed" -b "/dreamworld/ngs_data/NIPT/N40/IRs/N40.dupless.bam" | grep -P "^all.*$" > "/tmp/tmpivovkxoj/not_capture.csv" 2022-09-09 20:26:18,824 INFO SimpleSubprocess CoverageStats.NotCaptureCoverage - 0:00:21