[2024-01-25 20:12:20,647] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference
[2024-01-25 20:12:21,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:21,768] [INFO] Task started: Prodigal
[2024-01-25 20:12:21,769] [INFO] Running command: gunzip -c /var/lib/cwl/stga73d43da-db5d-4c0a-a5f8-0bc064468270/GCF_027625995.1_ASM2762599v1_genomic.fna.gz | prodigal -d GCF_027625995.1_ASM2762599v1_genomic.fna/cds.fna -a GCF_027625995.1_ASM2762599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:46,268] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:46,269] [INFO] Task started: HMMsearch
[2024-01-25 20:12:46,269] [INFO] Running command: hmmsearch --tblout GCF_027625995.1_ASM2762599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/reference_markers.hmm GCF_027625995.1_ASM2762599v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:46,522] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:46,523] [INFO] Found 6/6 markers.
[2024-01-25 20:12:46,560] [INFO] Query marker FASTA was written to GCF_027625995.1_ASM2762599v1_genomic.fna/markers.fasta
[2024-01-25 20:12:46,560] [INFO] Task started: Blastn
[2024-01-25 20:12:46,560] [INFO] Running command: blastn -query GCF_027625995.1_ASM2762599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/reference_markers.fasta -out GCF_027625995.1_ASM2762599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:47,170] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:47,173] [INFO] Selected 18 target genomes.
[2024-01-25 20:12:47,173] [INFO] Target genome list was writen to GCF_027625995.1_ASM2762599v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:47,182] [INFO] Task started: fastANI
[2024-01-25 20:12:47,183] [INFO] Running command: fastANI --query /var/lib/cwl/stga73d43da-db5d-4c0a-a5f8-0bc064468270/GCF_027625995.1_ASM2762599v1_genomic.fna.gz --refList GCF_027625995.1_ASM2762599v1_genomic.fna/target_genomes.txt --output GCF_027625995.1_ASM2762599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:09,419] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:09,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:09,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:09,431] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:09,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:09,431] [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 psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	84.3752	1105	1641	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	84.2078	1126	1641	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	83.7736	1089	1641	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	83.5208	1038	1641	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	83.4823	1022	1641	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	83.2537	1065	1641	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	82.1949	997	1641	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	82.1728	983	1641	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	82.1057	971	1641	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	82.0224	1035	1641	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	81.8247	940	1641	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	81.6718	1038	1641	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.5753	954	1641	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	81.389	924	1641	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	81.1542	1008	1641	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.6843	863	1641	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.5608	925	1641	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	80.2843	874	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:09,434] [INFO] DFAST Taxonomy check result was written to GCF_027625995.1_ASM2762599v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:09,434] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:09,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:09,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/checkm_data
[2024-01-25 20:13:09,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:09,483] [INFO] Task started: CheckM
[2024-01-25 20:13:09,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027625995.1_ASM2762599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027625995.1_ASM2762599v1_genomic.fna/checkm_input GCF_027625995.1_ASM2762599v1_genomic.fna/checkm_result
[2024-01-25 20:14:11,663] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:11,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:11,680] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:11,680] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:11,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027625995.1_ASM2762599v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:11,681] [INFO] Task started: Blastn
[2024-01-25 20:14:11,681] [INFO] Running command: blastn -query GCF_027625995.1_ASM2762599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b6aae9-0d6e-45dc-ab0e-0952ff1c3e12/dqc_reference/reference_markers_gtdb.fasta -out GCF_027625995.1_ASM2762599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:12,626] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:12,629] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:12,629] [INFO] Target genome list was writen to GCF_027625995.1_ASM2762599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:12,638] [INFO] Task started: fastANI
[2024-01-25 20:14:12,638] [INFO] Running command: fastANI --query /var/lib/cwl/stga73d43da-db5d-4c0a-a5f8-0bc064468270/GCF_027625995.1_ASM2762599v1_genomic.fna.gz --refList GCF_027625995.1_ASM2762599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027625995.1_ASM2762599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:28,435] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:28,443] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:14:28,444] [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_000737515.1	s__Hymenobacter sp000737515	93.9057	1433	1641	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	88.21	1287	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	84.3909	1103	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018145755.1	s__Hymenobacter sp018145755	84.2079	1126	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003944765.1	s__Hymenobacter perfusus	83.7951	1086	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576555.1	s__Hymenobacter swuensis	83.5045	1021	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	83.2161	1070	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250515.1	s__Hymenobacter sp014250515	83.138	1034	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	82.219	993	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	82.0219	1035	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	81.9082	994	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640315.1	s__Hymenobacter glacieicola	81.3863	925	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	81.1359	1012	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:28,445] [INFO] GTDB search result was written to GCF_027625995.1_ASM2762599v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:28,445] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:28,449] [INFO] DFAST_QC result json was written to GCF_027625995.1_ASM2762599v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:28,449] [INFO] DFAST_QC completed!
[2024-01-25 20:14:28,449] [INFO] Total running time: 0h2m8s