[2024-01-24 14:30:59,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference
[2024-01-24 14:31:00,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,857] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb1c720f-5244-4016-9b5d-45e40bf07d95/GCF_002105465.1_ASM210546v1_genomic.fna.gz | prodigal -d GCF_002105465.1_ASM210546v1_genomic.fna/cds.fna -a GCF_002105465.1_ASM210546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,817] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,818] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,818] [INFO] Running command: hmmsearch --tblout GCF_002105465.1_ASM210546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/reference_markers.hmm GCF_002105465.1_ASM210546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:13,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:13,123] [INFO] Found 6/6 markers.
[2024-01-24 14:31:13,161] [INFO] Query marker FASTA was written to GCF_002105465.1_ASM210546v1_genomic.fna/markers.fasta
[2024-01-24 14:31:13,161] [INFO] Task started: Blastn
[2024-01-24 14:31:13,162] [INFO] Running command: blastn -query GCF_002105465.1_ASM210546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/reference_markers.fasta -out GCF_002105465.1_ASM210546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,940] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,943] [INFO] Selected 27 target genomes.
[2024-01-24 14:31:13,944] [INFO] Target genome list was writen to GCF_002105465.1_ASM210546v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,969] [INFO] Task started: fastANI
[2024-01-24 14:31:13,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1c720f-5244-4016-9b5d-45e40bf07d95/GCF_002105465.1_ASM210546v1_genomic.fna.gz --refList GCF_002105465.1_ASM210546v1_genomic.fna/target_genomes.txt --output GCF_002105465.1_ASM210546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:31,796] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:31,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:31,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:31,802] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:31,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:31,803] [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
Aquidulcibacter paucihalophilus	strain=TH1-2	GCA_002105465.1	1978549	1978549	type	True	100.0	1165	1175	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:31:31,805] [INFO] DFAST Taxonomy check result was written to GCF_002105465.1_ASM210546v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:31,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:31,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:31,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/checkm_data
[2024-01-24 14:31:31,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:31,858] [INFO] Task started: CheckM
[2024-01-24 14:31:31,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002105465.1_ASM210546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002105465.1_ASM210546v1_genomic.fna/checkm_input GCF_002105465.1_ASM210546v1_genomic.fna/checkm_result
[2024-01-24 14:32:09,944] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:09,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:09,968] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:09,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:09,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002105465.1_ASM210546v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:09,969] [INFO] Task started: Blastn
[2024-01-24 14:32:09,969] [INFO] Running command: blastn -query GCF_002105465.1_ASM210546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc40694ad-6cc2-43f0-9512-900e2e4a73c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002105465.1_ASM210546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:11,143] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:11,152] [INFO] Selected 19 target genomes.
[2024-01-24 14:32:11,153] [INFO] Target genome list was writen to GCF_002105465.1_ASM210546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:11,180] [INFO] Task started: fastANI
[2024-01-24 14:32:11,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1c720f-5244-4016-9b5d-45e40bf07d95/GCF_002105465.1_ASM210546v1_genomic.fna.gz --refList GCF_002105465.1_ASM210546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002105465.1_ASM210546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:24,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:24,155] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:24,155] [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
GCF_002105465.1	s__Aquidulcibacter paucihalophilus	100.0	1165	1175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Aquidulcibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001602435.1	s__Aquidulcibacter sp001602435	83.7661	847	1175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Aquidulcibacter	95.0	99.04	98.12	0.91	0.87	3	-
GCF_003112735.1	s__Aquidulcibacter bacilliformis	80.8739	521	1175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Aquidulcibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:24,157] [INFO] GTDB search result was written to GCF_002105465.1_ASM210546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:24,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:24,161] [INFO] DFAST_QC result json was written to GCF_002105465.1_ASM210546v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:24,161] [INFO] DFAST_QC completed!
[2024-01-24 14:32:24,161] [INFO] Total running time: 0h1m25s