[2024-01-24 12:31:32,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:32,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:32,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference
[2024-01-24 12:31:33,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:33,924] [INFO] Task started: Prodigal
[2024-01-24 12:31:33,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgd03668ce-7bff-4581-8d18-a208d1f65190/GCF_022631375.1_ASM2263137v1_genomic.fna.gz | prodigal -d GCF_022631375.1_ASM2263137v1_genomic.fna/cds.fna -a GCF_022631375.1_ASM2263137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:01,656] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:01,656] [INFO] Task started: HMMsearch
[2024-01-24 12:32:01,656] [INFO] Running command: hmmsearch --tblout GCF_022631375.1_ASM2263137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/reference_markers.hmm GCF_022631375.1_ASM2263137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:01,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:01,884] [INFO] Found 6/6 markers.
[2024-01-24 12:32:01,923] [INFO] Query marker FASTA was written to GCF_022631375.1_ASM2263137v1_genomic.fna/markers.fasta
[2024-01-24 12:32:01,923] [INFO] Task started: Blastn
[2024-01-24 12:32:01,923] [INFO] Running command: blastn -query GCF_022631375.1_ASM2263137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/reference_markers.fasta -out GCF_022631375.1_ASM2263137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:02,500] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:02,503] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:02,503] [INFO] Target genome list was writen to GCF_022631375.1_ASM2263137v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:02,508] [INFO] Task started: fastANI
[2024-01-24 12:32:02,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgd03668ce-7bff-4581-8d18-a208d1f65190/GCF_022631375.1_ASM2263137v1_genomic.fna.gz --refList GCF_022631375.1_ASM2263137v1_genomic.fna/target_genomes.txt --output GCF_022631375.1_ASM2263137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:22,886] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:22,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:22,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:22,897] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:22,897] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:22,898] [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
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	85.6715	1271	1777	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	84.9458	1236	1777	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	84.747	1249	1777	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	84.5354	1204	1777	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.5103	1243	1777	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	84.5027	1249	1777	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.2987	1095	1777	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	83.0099	1086	1777	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	82.9208	1012	1777	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	82.7488	1008	1777	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.4156	1051	1777	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.0129	944	1777	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.2984	753	1777	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.0304	708	1777	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	74.8565	67	1777	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	74.634	62	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:22,899] [INFO] DFAST Taxonomy check result was written to GCF_022631375.1_ASM2263137v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:22,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:22,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:22,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/checkm_data
[2024-01-24 12:32:22,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:22,951] [INFO] Task started: CheckM
[2024-01-24 12:32:22,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022631375.1_ASM2263137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022631375.1_ASM2263137v1_genomic.fna/checkm_input GCF_022631375.1_ASM2263137v1_genomic.fna/checkm_result
[2024-01-24 12:33:31,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:31,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:31,687] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:31,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:31,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022631375.1_ASM2263137v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:31,687] [INFO] Task started: Blastn
[2024-01-24 12:33:31,687] [INFO] Running command: blastn -query GCF_022631375.1_ASM2263137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904f22ef-c9f3-4fe1-b95e-48354addcdd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_022631375.1_ASM2263137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:32,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:32,564] [INFO] Selected 18 target genomes.
[2024-01-24 12:33:32,564] [INFO] Target genome list was writen to GCF_022631375.1_ASM2263137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:32,572] [INFO] Task started: fastANI
[2024-01-24 12:33:32,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgd03668ce-7bff-4581-8d18-a208d1f65190/GCF_022631375.1_ASM2263137v1_genomic.fna.gz --refList GCF_022631375.1_ASM2263137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022631375.1_ASM2263137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:54,910] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:54,921] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:54,922] [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_016056375.1	s__Hymenobacter negativus_A	85.8317	1267	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_012275535.1	s__Hymenobacter artigasi	85.6747	1271	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	85.2187	1208	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_016427455.1	s__Hymenobacter sp016427455	85.0772	1231	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_015694525.1	s__Hymenobacter ruricola	84.7369	1251	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734815.1	s__Hymenobacter rubidus	84.5609	1201	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694735.1	s__Hymenobacter properus	84.5186	1247	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640435.1	s__Hymenobacter frigidus	83.3007	1094	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	83.0117	1085	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571495.1	s__Hymenobacter negativus	82.9516	1231	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	82.9348	1076	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816145.1	s__Hymenobacter lapidarius	82.9021	1015	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	82.7515	1008	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	82.4187	1051	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	81.7838	1026	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699115.1	s__Hymenobacter sp014699115	81.032	942	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	79.3065	734	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	78.9399	608	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:54,923] [INFO] GTDB search result was written to GCF_022631375.1_ASM2263137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:54,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:54,927] [INFO] DFAST_QC result json was written to GCF_022631375.1_ASM2263137v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:54,927] [INFO] DFAST_QC completed!
[2024-01-24 12:33:54,927] [INFO] Total running time: 0h2m22s