Genome Informatics Laboratory at KRIBB

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====== ZGA log file example ======

KNA 'genome'의 메타데이터에 넣어야 하는 상당수의 정보가 이 파일에 들어 있다. Genome completeness/contamination/heterogeneity에 문제가 있는 경우 - WARNING - 이 표시된다.

  2025-02-07 10:08:20,906 - INFO - ZGA ver. 0.0.9post2
  2025-02-07 10:08:20,906 - INFO - Full log location: /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/zga.log
  2025-02-07 10:08:20,906 - INFO - Checking input files.
  2025-02-07 10:08:20,906 - DEBUG - Input reads: [{'type': 'short', 'forward': '/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_1.fastq', 'reverse': '/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_2.fastq'}]
  2025-02-07 10:08:20,906 - INFO - Read quality control started
  2025-02-07 10:08:20,906 - DEBUG - QC of /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_1.fastq
  2025-02-07 10:08:20,906 - DEBUG - Running: fastp -L -Q -G -A -z 1 --stdout -w 16 -i /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_1.fastq -h /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/readQC/12221T_1.fastq.html -j /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/readQC/12221T_1.fastq.json
  2025-02-07 10:08:23,502 - DEBUG - QC of /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_2.fastq
  2025-02-07 10:08:23,502 - DEBUG - Running: fastp -L -Q -G -A -z 1 --stdout -w 16 -i /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_2.fastq -h /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/readQC/12221T_2.fastq.html -j /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/readQC/12221T_2.fastq.json
  2025-02-07 10:08:26,143 - INFO - Reads processing started
  2025-02-07 10:08:26,144 - INFO - Trimming and filtering paired end reads
  2025-02-07 10:08:26,144 - DEBUG - Running: bbduk.sh Xmx=8G t=16 ref=/home/hyjeong/miniconda3/envs/zga/lib/python3.8/site-packages/zga/data/sr.adapters.fasta k=19 ktrim=r qtrim=r trimq=18 entropy=-1 minlength=33 in=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_1.fastq in2=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/02_renamed_fastq_files/12221T_2.fastq out=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r1.fq out2=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r2.fq stats=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.bbduk.pe.txt
  2025-02-07 10:08:28,105 - INFO - Merging paired-end reads.
  2025-02-07 10:08:28,105 - DEBUG - Running: bbmerge.sh Xmx=8G t=16 in=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r1.fq in2=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r2.fq outu1=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u1.fq.gz outu2=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u2.fq.gz out=/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.merged.fq.gz strict=t
  2025-02-07 10:08:36,647 - DEBUG - Removing /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r1.fq
  2025-02-07 10:08:36,840 - DEBUG - Removing /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.r2.fq
  2025-02-07 10:08:37,019 - INFO - Read processing finished
  2025-02-07 10:08:37,019 - DEBUG - Processed reads: [{'type': 'short', 'forward': '/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u1.fq.gz', 'reverse': '/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u2.fq.gz', 'merged': '/data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.merged.fq.gz'}]
  2025-02-07 10:08:37,019 - INFO - Estimating genome size with mash using: /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u1.fq.gz, /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u2.fq.gz, /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.merged.fq.gz
  2025-02-07 10:08:37,019 - DEBUG - Running: mash sketch -r -m 10 -o /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/sketch /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u1.fq.gz /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u2.fq.gz /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.merged.fq.gz
  2025-02-07 10:08:53,975 - INFO - Estimated genome size is 4527120 bp at coverage 103.766.
  2025-02-07 10:08:53,975 - INFO - Assembling started
  2025-02-07 10:08:54,017 - DEBUG - Unicycler version 0.5.0 available.
  2025-02-07 10:08:54,017 - DEBUG - Running: unicycler -o /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/assembly -t 16 --mode normal -1 /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u1.fq.gz -2 /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.u2.fq.gz -s /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/reads/lib1.merged.fq.gz
  2025-02-07 10:27:33,760 - INFO - Assembling finished
  2025-02-07 10:27:33,785 - INFO - Assembly length: 4468484
  2025-02-07 10:27:33,786 - INFO - Contig count: 87
  2025-02-07 10:27:33,786 - INFO - N50: 284033
  2025-02-07 10:27:33,786 - INFO - Checking genome quality
  2025-02-07 10:27:36,403 - INFO - Bacteria marker set will be used for CheckM
  2025-02-07 10:27:36,403 - DEBUG - Running: checkm taxonomy_wf -f /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/checkm.result.txt -x .fasta -t 16 domain Bacteria /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/checkm_tmp_in /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/checkm
  2025-02-07 10:27:58,987 - INFO - Genome completeness: 98.28%
  2025-02-07 10:27:58,987 - INFO - Genome contamination: 0.0%
  2025-02-07 10:27:58,987 - INFO - Genome heterogeneity: 0.0%
  2025-02-07 10:27:58,987 - INFO - Genome annotation started
  2025-02-07 10:27:59,069 - DEBUG - DFAST version 1.2.17 available.
  2025-02-07 10:27:59,069 - INFO - No locus tag provided. Generating it as MD5 hash of genome
  2025-02-07 10:27:59,080 - INFO - Locus tag generated: HPEMQL
  2025-02-07 10:27:59,080 - DEBUG - Running: dfast -g /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/assembly/assembly.fasta -o /data/project/52_KCTC_72_microbial_genomes_2014_Apr/01_Illumina_2014-04-16/09_47_samples_zga_again/zga_12221T/annotation --organism Unknown sp. --cpu 16 --locus_tag_prefix HPEMQL --step 10
  2025-02-07 10:28:42,594 - INFO - Workflow finished!