2022-09-09 19:57:05,511 INFO Cutadapt Mode: Paired-end 2022-09-09 19:57:05,512 INFO Cutadapt Input FASTQ [R1]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N29/N29_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz 2022-09-09 19:57:05,512 INFO Cutadapt Input FASTQ [R2]: /dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N29/N29_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz 2022-09-09 19:57:05,512 INFO Cutadapt Output FASTQ [R1]: /tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz 2022-09-09 19:57:05,512 INFO Cutadapt Output FASTQ [R2]: /tmp/tmpuzw47b8t/adapter_R2_0.fastq.gz 2022-09-09 19:57:05,512 INFO Cutadapt Adapter: illumina 2022-09-09 19:57:05,513 DEBUG SimpleSubprocess cutadapt -j 10 -e 0.2 -m 8 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o "/tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz" -p "/tmp/tmpuzw47b8t/adapter_R2_0.fastq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N29/N29_FKDL220180557-1A_HJCT5DSX3_L1_1.fq.gz" "/dreamworld/ngs_data/20220816_Novogene_data/X201SC22041027-Z01-F003/01.RawData/N29/N29_FKDL220180557-1A_HJCT5DSX3_L1_2.fq.gz" > "/dreamworld/ngs_data/NIPT/N29/N29.InputItem0.cutadapt.txt" 2022-09-09 19:57:13,224 INFO SimpleSubprocess Cutadapt.Trim - 0:00:07 2022-09-09 19:57:13,224 INFO FastQC FastQ: /tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz 2022-09-09 19:57:13,224 INFO FastQC Report: /dreamworld/ngs_data/NIPT/N29/N29.InputItem0.fastqc.html 2022-09-09 19:57:13,226 INFO FastQC Subsample: 1000000 2022-09-09 19:57:13,226 DEBUG SimpleSubprocess zcat -q "/tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz" | head -4000000 | gzip -c > "/tmp/tmp5ugt9vc2/sample.fastq.gz" 2022-09-09 19:57:23,559 INFO SimpleSubprocess FastQC.Sampling - 0:00:10 2022-09-09 19:57:23,560 DEBUG SimpleSubprocess fastqc -o "/tmp/tmp5ugt9vc2" -t 10 "/tmp/tmp5ugt9vc2/sample.fastq.gz" 2022-09-09 19:57:28,842 INFO SimpleSubprocess FastQC.Analysis - 0:00:05 2022-09-09 19:57:28,882 DEBUG SimpleSubprocess cp "/tmp/tmp5ugt9vc2/sample_fastqc.html" "/dreamworld/ngs_data/NIPT/N29/N29.InputItem0.fastqc.html" 2022-09-09 19:57:28,886 INFO SimpleSubprocess FastQC.Move - 0:00:00 2022-09-09 19:57:28,892 INFO BWA R1: /tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz 2022-09-09 19:57:28,893 INFO BWA R2: /tmp/tmpuzw47b8t/adapter_R2_0.fastq.gz 2022-09-09 19:57:28,893 INFO BWA Output BAM: /tmp/tmpuzw47b8t/temp_0.bam 2022-09-09 19:57:28,893 INFO BWA Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 19:57:28,893 INFO BWA RG Header: @RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.TTAGGCAT\tLB:LIB-N29-001\tSM:N29 2022-09-09 19:57:28,893 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; set -o pipefail; bwa mem -R "@RG\tID:FCHJCT5DSX3.L1\tPL:ILLUMINA\tPU:FCHJCT5DSX3.L1.TTAGGCAT\tLB:LIB-N29-001\tSM:N29" -t 10 -v 1 "/dreamworld/databases/hg19_canonical/hg19_canonical.fa" "/tmp/tmpuzw47b8t/adapter_R1_0.fastq.gz" "/tmp/tmpuzw47b8t/adapter_R2_0.fastq.gz" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmpgl67mzk3" -SO queryname -I "/dev/stdin" -O "/tmp/tmpuzw47b8t/temp_0.bam" 2022-09-09 19:58:34,390 INFO SimpleSubprocess BWA.AlignAndSort - 0:01:05 2022-09-09 19:58:34,390 DEBUG SimpleSubprocess cp "/tmp/tmpuzw47b8t/temp_0.bam" "/dreamworld/ngs_data/NIPT/N29/IRs/N29.primary.bam" 2022-09-09 19:58:34,454 INFO SimpleSubprocess DaemonicPipe.CopyBAM - 0:00:00 2022-09-09 19:58:34,454 DEBUG SimpleSubprocess samtools flagstat -O tsv "/dreamworld/ngs_data/NIPT/N29/IRs/N29.primary.bam" > "/dreamworld/ngs_data/NIPT/N29/N29.primary_stats.txt" 2022-09-09 19:58:35,246 INFO SimpleSubprocess DaemonicPipe.FlagStats - 0:00:00 2022-09-09 19:58:35,270 INFO MarkDuplicates Input: /dreamworld/ngs_data/NIPT/N29/IRs/N29.primary.bam 2022-09-09 19:58:35,270 INFO MarkDuplicates Output: /dreamworld/ngs_data/NIPT/N29/IRs/N29.dupless.bam 2022-09-09 19:58:35,270 INFO MarkDuplicates Metrics: /dreamworld/ngs_data/NIPT/N29/N29.md_metrics.txt 2022-09-09 19:58:35,270 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/tmp3foemyg_" -M "/dreamworld/ngs_data/NIPT/N29/N29.md_metrics.txt" -I "/dreamworld/ngs_data/NIPT/N29/IRs/N29.primary.bam" -O "/dev/stdout" | gatk SortSam --VERBOSITY ERROR --TMP_DIR "/tmp/tmp3foemyg_" -SO coordinate -I "/dev/stdin" -O "/dreamworld/ngs_data/NIPT/N29/IRs/N29.dupless.bam" 2022-09-09 19:58:52,745 INFO SimpleSubprocess MarkDuplicates.RemoveAndSort - 0:00:17 2022-09-09 19:58:52,745 DEBUG SimpleSubprocess source /dreamworld/miniconda3/bin/activate gatk; gatk BuildBamIndex -I "/dreamworld/ngs_data/NIPT/N29/IRs/N29.dupless.bam" 2022-09-09 19:58:58,879 INFO SimpleSubprocess MarkDuplicates.Index - 0:00:06 2022-09-09 19:58:58,880 INFO CoverageStats BAM File: /dreamworld/ngs_data/NIPT/N29/IRs/N29.dupless.bam 2022-09-09 19:58:58,880 INFO CoverageStats Reference: /dreamworld/databases/hg19_canonical/hg19_canonical.fa 2022-09-09 19:58:58,880 INFO CoverageStats Capture BED: /dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed 2022-09-09 19:58:58,880 DEBUG SimpleSubprocess awk 'BEGIN {FS="\t"}; {print $1 FS "0" FS $2}' "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" > "/tmp/tmp3o11ttjx/genome.bed" 2022-09-09 19:58:58,884 INFO SimpleSubprocess PrepareGenomeBED.Create - 0:00:00 2022-09-09 19:58:58,884 DEBUG SimpleSubprocess bedtools subtract -a "/tmp/tmp3o11ttjx/genome.bed" -b "/dreamworld/databases/hg19_canonical/capture/KAPA_HyperExome/KAPA_HyperExome.capture.bed" | sed -e 's/$/\t\./' > "/tmp/tmp3o11ttjx/not_capture.bed" 2022-09-09 19:59:01,295 INFO SimpleSubprocess CoverageStats.CreateNotCaptureBed - 0:00:02 2022-09-09 19:59:01,295 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/N29/IRs/N29.dupless.bam" | grep -P "^all.*$" > "/tmp/tmp3o11ttjx/capture.csv" 2022-09-09 19:59:03,860 INFO SimpleSubprocess CoverageStats.CaptureCoverage - 0:00:02 2022-09-09 19:59:03,860 DEBUG SimpleSubprocess bedtools coverage -hist -sorted -g "/dreamworld/databases/hg19_canonical/hg19_canonical.fa.fai" -a "/tmp/tmp3o11ttjx/not_capture.bed" -b "/dreamworld/ngs_data/NIPT/N29/IRs/N29.dupless.bam" | grep -P "^all.*$" > "/tmp/tmp3o11ttjx/not_capture.csv" 2022-09-09 19:59:25,227 INFO SimpleSubprocess CoverageStats.NotCaptureCoverage - 0:00:21