Remove reads with a quality score below a certain threshold and filter out reads corresponding to the lambda phage control sequence used in Nanopore sequencing.
@20287416-6962-4e5f-a6bc-58d29c322999 qs:f:23.9827 st:Z:2025-02-27T22:52:32.999+00:00 RG:Z:19b6eeae4e187e96276e1e2f623fecff1ced9c75_dna_r10.4.1_e8.2_400bps_sup@v5.0.0_SQK-NBD114-24_barcode01
TGTGGACGGCTCTGGGACCCTCACTGAGAACGAGTTCAACGCCCAGGCGGCCTCCCGACTGCAGAAGCTCGGTGTCGACGAGGTGAGGAGATAGTGGCAATTTTGGAGTGCTCAGGATGTCGTGGCGGTGGCGTTCCAAATAATAGACTCCTCGGGGCACGGCTGCATAGACCAGGACGAGTTCGTCCAAATGCTGCTGAAGATGCTGCACCCCCCGAGCGCGCAGGATCTGCTACTGGTCCAGAAGAACTTGACCATGGTCCAGAACCTGTTGGCGGAGCACATGAAGAAAACGGCGATCCGCCACAAGAACATCGAAACCAAGCTCGACCGCCTGCTCGGCAGACGGCCCGGCGGGGACCTCTCGCGAATGGGCTCGGAGAGGATGTCCAGCACGGGCTCGTTGGACGCGGAGACTCGGGAGGCTGTGAACCAGCTCCTGGGGAAAACGTGAACGCATGGCACACTGTTGGTTTCCAATACCACTGTCATCCTATCGGCTTGCGTCCATAGTGGTAATCGCCGGTGAGTCACACCTGCTCGTTGCACTGCTATTTGTTATAGTCGGCAGTGTTACCGCTCGGCGAGGGGCGCAGCGGGTGCGGCAAGGTCCCCAGCGAGAGACTGACGGTTACCCAGAATATAGGGCGCGGCGTGGCGCGGGTGACGACAATTGCCCATCGTCTTCGCTATTGCCCCAACGGTCTCAGACGTACTTCTGTCCATGCCCTGCTGGAGCAAATTGCCATGTTGGCCGAACCCTCCTGCAGCTAATGCAGCCCCGGGTTCTGCTATCCGTAGTAGCATTGGTATCTCCTCAGCTCTGACCTTCACTACCGTGCGCGGATCACCGGCGCACGCGTGCAGGTGAGTGATTTTGTTGTATAGAGCCCTTCTGTTGGTGTGTTGTAGTATATAAGATAGCCCGAGGCTGTCGGCTCTGCCGATTCAAGGGCTTCTTCCCCGCTACGCTCTATTATTTCTCATTCGACTCTATTTCAAATGAGTTGTGCGCTGCTTGTATAGCTAATCGATATATGCTTTAGCTCAGGCAAAACATTGCTCTGGTTGCGCACATCGTCGGTTATTACAAGCCCACTCATTATCCATATGGCCCCCAAGTTGCGTTCCGTTAGAGGTATCACTGATCCGAGGGTGCAGGAGGACTCGGGTGAACACACCGACGGCAGTGCTTTCTACTCGGGCGCTGAGACTCACTCACAGGCTTGATCATCGGCGTGGCATCAGTACTGACAGTACAGTGTGACCTTCAATGGCCCTCTTACTGTTCTTCTTCTTGCCTCTACTGGCCTCGGGCGCTGACTACTGCTCCAGGACCCAGCAGGGCATCCCACTCTCTCCGGGAGGACCGTATAATACTAGCGGTGGTCCCATCCTGGACGACCCACGAATCATCAATGTAACTAAGTCGAGAGCCACGTGTTAACGTGCAGGTGCACCTGGTGCCGCACACTCACGACGACGTGGGGTGGTTGAAGACGGTCGACCAGTACTTTACAGGTGCCCGCCGCCCCCCCCCCTTTCTTACAGGCCACAGGCACTTACAATAAGATAAGGAGCGCCAACGTGGGCCTTATCATAGACTCTGTGGTTGATGAGCTCGTTAAGGACGAGAACAGGAGATTCATCTACGTGGAGATGGTCAGGCCTGCACCACCGTCCCGGCCAGTCTCTTAGGCTTTCTTTCACCGATGGTGGCGCCGCCAGTCCACGGTGAGGAGAAGGGTCGTGAGGAAGCTGGTGGCCGAGGGGCGCTTGGAGTTCGTCAACGCGGGCTGGGTGATGAACGACGAGGCCTCCACCATGTACACGGATATCATAGATCAGCACACAGCCGGTACCGGCGCACGTGGAGCTTCCCATTCCTCACAGGGGCGCTGGAAGTTGGATAGAGTTCTCCACGGCGGCCTCTCCTCGGATCGGGTGGCAGATCGACCCCCTCGGCCACTCAGCGTTCCAGAACAAAGCATTCAAGCAGGTATCCCGTCGCTGAACGCTGCCTTTAATTCCCCAGATGGGTTTCGATGGGTGGATGGTTGGCAGGGCCGACGCTCAGGACATGGCCATAAGGGAGGCCTACGGCGCCCTCGAGATGGTCATTAAAGCGCACTGTGAAGGTAGCGTGCTCCCCGCAGGTATATCACACCGGCAACTCTTCTACGGACGGCATCTTCATGGGGCTCATGCACATGTAGGCGCTCCGCTCCGCTAGAGTACTCTGAAATTCCGAGGTACTCGCCGCCTGAAAGCTTCGACTTCGAGATCGGCTCTGGTGATTCTCCTCTCTGCGATGACCCTCTAATAGAGGGACTTAATATTGACAGCCGACTGGACGGTCTCAGGAGAGTGAGACGTGGCCGGCTTCGACGCGGATACTCTTCCCCAGATCGCGATGCAGCAATCTGATATGTACAACCCCGTCGGGAAGGGGAAGGGCAGCAAGAACATCATATTCACCATGGTGCAGCTGTTTGGGGACTCGGCGGTTCCCGGACCTTAGGGGATGGACTTCAACTACCAGCAGGCTAAGACGTGGTACGGCAACATGGACAAGCTCATCCACTACACCAAGCTGGCAGAGGAAGAGAAGATGAAGAATAGCAGCTTCGAGGGACCGATCATCAATGTCTTTTATAGCAACCCAAGGTGGGGCAATGGCCAGGAATGGGTGGCTTCTTCGTGTTTGGCAAATTGTATTATTGTGGCCGCCGAAGGCTCCGAGCTGTTTGCCTTCCCGGCTGGTGTCAGTTAGCTCTCAGGACATACATTGAATCTCGGCATTATCAATnanopore~filter-lambda-phage-reads -c 8 -m 32 input_1/
pp nanopore~filter-lambda-phage-reads -c 8 -m 32 input_1/
PID: 2301864
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'nanopore~filter-lambda-phage-reads' -c 8 -m 32 input_1/
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/nanopore~filter-lambda-phage-reads
Containers: c2997108/minimap2:2.28_lambda-phage centos:centos6 quay.io/biocontainers/samtools:1.19--h50ea8bc_0 rtibiocloud/pigz:v2.4_b243f9
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ awk -v qt=10 '
{if(NR%4==1){q=99; for(i=1;i<=NF;i++){if($i~"^qs:f:"){q=substr($i,6)}}; if(q>=qt){vis=1}else{vis=0}}; if(vis==1){print $0}}
'
+ FUNC_RUN_DOCKER c2997108/minimap2:2.28_lambda-phage minimap2 -ax map-ont -t 8 /usr/local/lambda.fasta /dev/stdin
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -b -f 4
+ PP_RUN_IMAGE=c2997108/minimap2:2.28_lambda-phage
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ find input_1// -maxdepth 1
++ grep -E '[.](fastq|fq)(|[.]gz)$'
+ FUNC_RUN_DOCKER rtibiocloud/pigz:v2.4_b243f9 pigz
++ date +%Y%m%d_%H%M%S_%3N
+ PP_RUN_IMAGE=rtibiocloud/pigz:v2.4_b243f9
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ FUNC_RUN_DOCKER quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools fastq
+ PP_RUN_IMAGE=quay.io/biocontainers/samtools:1.19--h50ea8bc_0
+ shift
+ PPDOCNAME=pp20250302_181622_677_16543
+ PP_RUN_DOCKER_CMD=("${@}")
+ echo pp20250302_181622_677_16543
+ PPDOCNAME=pp20250302_181622_678_19569
++ date +%Y%m%d_%H%M%S_%3N
+ echo pp20250302_181622_678_19569
++ id -u
+ PPDOCNAME=pp20250302_181622_678_28640
+ echo pp20250302_181622_678_28640
++ id -u
++ id -u
+ for i in `find "$input_1"/ -maxdepth 1 |grep -E '[.](fastq|fq)(|[.]gz)$' || true`
+ PPDOCNAME=pp20250302_181622_681_6903
+ echo pp20250302_181622_681_6903
++ echo input_1//PBC33536_pass_barcode01_51e6008e_d3103f53_0.fastq.gz
++ grep '[.]gz$'
++ id -u
++ wc -l
++ id -g
++ id -g
++ id -g
+ docker run --name pp20250302_181622_678_19569 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools view -b -f 4
+ '[' 1 = 1 ']'
+ docker run --name pp20250302_181622_677_16543 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/minimap2:2.28_lambda-phage minimap2 -ax map-ont -t 8 /usr/local/lambda.fasta /dev/stdin
+ zcat input_1//PBC33536_pass_barcode01_51e6008e_d3103f53_0.fastq.gz
++ id -g
+ docker run --name pp20250302_181622_678_28640 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm rtibiocloud/pigz:v2.4_b243f9 pigz
+ docker run --name pp20250302_181622_681_6903 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/samtools:1.19--h50ea8bc_0 samtools fastq
[M::mm_idx_gen::0.004*14.38] collected minimizers
[M::mm_idx_gen::0.005*11.92] sorted minimizers
[M::main::0.005*11.84] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.006*10.47] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.007*9.47] distinct minimizers: 9041 (99.99% are singletons); average occurrences: 1.000; average spacing: 5.364; total length: 48502
+ for i in `find "$input_1"/ -maxdepth 1 |grep -E '[.](fastq|fq)(|[.]gz)$' || true`
++ echo input_1//test.fq
++ wc -l
++ grep '[.]gz$'
++ true
+ '[' 0 = 1 ']'
+ cat input_1//test.fq
[M::worker_pipeline::1.603*0.86] mapped 6451 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -ax map-ont -t 8 /usr/local/lambda.fasta /dev/stdin
[M::main] Real time: 1.607 sec; CPU: 1.385 sec; Peak RSS: 0.045 GB
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 6406 reads
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/nanopore~filter-lambda-phage-reads/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit