[2023-06-28 17:55:51,916] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:55:51,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:55:51,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference
[2023-06-28 17:55:53,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:55:53,351] [INFO] Task started: Prodigal
[2023-06-28 17:55:53,351] [INFO] Running command: gunzip -c /var/lib/cwl/stged83ddee-b0d2-4ea1-9d73-cc75a21396ec/GCA_020062945.1_ASM2006294v1_genomic.fna.gz | prodigal -d GCA_020062945.1_ASM2006294v1_genomic.fna/cds.fna -a GCA_020062945.1_ASM2006294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:55:54,596] [INFO] Task succeeded: Prodigal
[2023-06-28 17:55:54,596] [INFO] Task started: HMMsearch
[2023-06-28 17:55:54,596] [INFO] Running command: hmmsearch --tblout GCA_020062945.1_ASM2006294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/reference_markers.hmm GCA_020062945.1_ASM2006294v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:55:54,728] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:55:54,729] [WARNING] Found 4/6 markers. [/var/lib/cwl/stged83ddee-b0d2-4ea1-9d73-cc75a21396ec/GCA_020062945.1_ASM2006294v1_genomic.fna.gz]
[2023-06-28 17:55:54,740] [INFO] Query marker FASTA was written to GCA_020062945.1_ASM2006294v1_genomic.fna/markers.fasta
[2023-06-28 17:55:54,740] [INFO] Task started: Blastn
[2023-06-28 17:55:54,741] [INFO] Running command: blastn -query GCA_020062945.1_ASM2006294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/reference_markers.fasta -out GCA_020062945.1_ASM2006294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:55:55,270] [INFO] Task succeeded: Blastn
[2023-06-28 17:55:55,276] [INFO] Selected 6 target genomes.
[2023-06-28 17:55:55,276] [INFO] Target genome list was writen to GCA_020062945.1_ASM2006294v1_genomic.fna/target_genomes.txt
[2023-06-28 17:55:55,278] [INFO] Task started: fastANI
[2023-06-28 17:55:55,279] [INFO] Running command: fastANI --query /var/lib/cwl/stged83ddee-b0d2-4ea1-9d73-cc75a21396ec/GCA_020062945.1_ASM2006294v1_genomic.fna.gz --refList GCA_020062945.1_ASM2006294v1_genomic.fna/target_genomes.txt --output GCA_020062945.1_ASM2006294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:55:57,128] [INFO] Task succeeded: fastANI
[2023-06-28 17:55:57,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:55:57,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:55:57,131] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:55:57,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:55:57,131] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-28 17:55:57,133] [INFO] DFAST Taxonomy check result was written to GCA_020062945.1_ASM2006294v1_genomic.fna/tc_result.tsv
[2023-06-28 17:55:57,134] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:55:57,134] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:55:57,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/checkm_data
[2023-06-28 17:55:57,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:55:57,146] [INFO] Task started: CheckM
[2023-06-28 17:55:57,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020062945.1_ASM2006294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020062945.1_ASM2006294v1_genomic.fna/checkm_input GCA_020062945.1_ASM2006294v1_genomic.fna/checkm_result
[2023-06-28 17:56:11,595] [INFO] Task succeeded: CheckM
[2023-06-28 17:56:11,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 9.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:56:11,622] [INFO] ===== Completeness check finished =====
[2023-06-28 17:56:11,622] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:56:11,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020062945.1_ASM2006294v1_genomic.fna/markers.fasta)
[2023-06-28 17:56:11,622] [INFO] Task started: Blastn
[2023-06-28 17:56:11,623] [INFO] Running command: blastn -query GCA_020062945.1_ASM2006294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5790021d-e878-4f1a-be3e-7935c8afec0d/dqc_reference/reference_markers_gtdb.fasta -out GCA_020062945.1_ASM2006294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:56:12,324] [INFO] Task succeeded: Blastn
[2023-06-28 17:56:12,329] [INFO] Selected 21 target genomes.
[2023-06-28 17:56:12,329] [INFO] Target genome list was writen to GCA_020062945.1_ASM2006294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:56:12,359] [INFO] Task started: fastANI
[2023-06-28 17:56:12,360] [INFO] Running command: fastANI --query /var/lib/cwl/stged83ddee-b0d2-4ea1-9d73-cc75a21396ec/GCA_020062945.1_ASM2006294v1_genomic.fna.gz --refList GCA_020062945.1_ASM2006294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020062945.1_ASM2006294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:56:17,035] [INFO] Task succeeded: fastANI
[2023-06-28 17:56:17,037] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:56:17,038] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
--------------------------------------------------------------------------------
[2023-06-28 17:56:17,040] [INFO] GTDB search result was written to GCA_020062945.1_ASM2006294v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:56:17,040] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:56:17,044] [INFO] DFAST_QC result json was written to GCA_020062945.1_ASM2006294v1_genomic.fna/dqc_result.json
[2023-06-28 17:56:17,045] [INFO] DFAST_QC completed!
[2023-06-28 17:56:17,045] [INFO] Total running time: 0h0m25s