[2024-01-24 13:31:56,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:56,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:56,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference
[2024-01-24 13:31:57,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:57,867] [INFO] Task started: Prodigal
[2024-01-24 13:31:57,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg30372846-dbd8-4d51-bcad-eb766f0397f6/GCF_001553545.1_ASM155354v1_genomic.fna.gz | prodigal -d GCF_001553545.1_ASM155354v1_genomic.fna/cds.fna -a GCF_001553545.1_ASM155354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:11,308] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:11,309] [INFO] Task started: HMMsearch
[2024-01-24 13:32:11,309] [INFO] Running command: hmmsearch --tblout GCF_001553545.1_ASM155354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/reference_markers.hmm GCF_001553545.1_ASM155354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:11,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:11,581] [INFO] Found 6/6 markers.
[2024-01-24 13:32:11,612] [INFO] Query marker FASTA was written to GCF_001553545.1_ASM155354v1_genomic.fna/markers.fasta
[2024-01-24 13:32:11,612] [INFO] Task started: Blastn
[2024-01-24 13:32:11,613] [INFO] Running command: blastn -query GCF_001553545.1_ASM155354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/reference_markers.fasta -out GCF_001553545.1_ASM155354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:12,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:12,233] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:12,233] [INFO] Target genome list was writen to GCF_001553545.1_ASM155354v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:12,276] [INFO] Task started: fastANI
[2024-01-24 13:32:12,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg30372846-dbd8-4d51-bcad-eb766f0397f6/GCF_001553545.1_ASM155354v1_genomic.fna.gz --refList GCF_001553545.1_ASM155354v1_genomic.fna/target_genomes.txt --output GCF_001553545.1_ASM155354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:20,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:20,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:20,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:20,663] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:20,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:20,664] [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
Capnocytophaga haemolytica	strain=CCUG 32990	GCA_001553545.1	45243	45243	type	True	100.0	895	896	95	conclusive
Capnocytophaga haemolytica	strain=NCTC12947	GCA_900187255.1	45243	45243	type	True	99.9953	896	896	95	conclusive
Capnocytophaga haemolytica	strain=DSM 11385	GCA_900115315.1	45243	45243	type	True	99.9627	859	896	95	conclusive
Capnocytophaga ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	80.9928	148	896	95	below_threshold
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	80.7954	148	896	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	78.9379	143	896	95	below_threshold
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	78.8571	157	896	95	below_threshold
Capnocytophaga granulosa	strain=DSM 11449	GCA_900106575.1	45242	45242	type	True	78.1925	50	896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:20,666] [INFO] DFAST Taxonomy check result was written to GCF_001553545.1_ASM155354v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:20,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:20,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:20,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/checkm_data
[2024-01-24 13:32:20,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:20,700] [INFO] Task started: CheckM
[2024-01-24 13:32:20,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001553545.1_ASM155354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001553545.1_ASM155354v1_genomic.fna/checkm_input GCF_001553545.1_ASM155354v1_genomic.fna/checkm_result
[2024-01-24 13:33:01,633] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:01,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,661] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:01,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:01,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001553545.1_ASM155354v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:01,662] [INFO] Task started: Blastn
[2024-01-24 13:33:01,662] [INFO] Running command: blastn -query GCF_001553545.1_ASM155354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f1a17f7-45f5-42c3-904e-47ea82dbed90/dqc_reference/reference_markers_gtdb.fasta -out GCF_001553545.1_ASM155354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,553] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,558] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:02,558] [INFO] Target genome list was writen to GCF_001553545.1_ASM155354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,599] [INFO] Task started: fastANI
[2024-01-24 13:33:02,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg30372846-dbd8-4d51-bcad-eb766f0397f6/GCF_001553545.1_ASM155354v1_genomic.fna.gz --refList GCF_001553545.1_ASM155354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001553545.1_ASM155354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:17,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,097] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:17,097] [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_001553545.1	s__Capnocytophaga haemolytica	100.0	896	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000023285.1	s__Capnocytophaga ochracea	80.9706	149	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
GCF_002209445.1	s__Capnocytophaga endodontalis	79.1283	157	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.66	96.51	0.90	0.87	9	-
GCF_002999135.1	s__Capnocytophaga sp002999135	78.9541	109	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900446695.1	s__Capnocytophaga sputigena	78.827	142	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.52	96.32	0.92	0.88	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:17,099] [INFO] GTDB search result was written to GCF_001553545.1_ASM155354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:17,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:17,103] [INFO] DFAST_QC result json was written to GCF_001553545.1_ASM155354v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:17,103] [INFO] DFAST_QC completed!
[2024-01-24 13:33:17,103] [INFO] Total running time: 0h1m21s