[2024-01-24 12:09:04,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:04,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:04,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference
[2024-01-24 12:09:06,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,063] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,063] [INFO] Running command: gunzip -c /var/lib/cwl/stg3499494a-e5be-4ff2-ab91-233ab5a629ed/GCF_020685205.1_ASM2068520v1_genomic.fna.gz | prodigal -d GCF_020685205.1_ASM2068520v1_genomic.fna/cds.fna -a GCF_020685205.1_ASM2068520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:33,016] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:33,017] [INFO] Task started: HMMsearch
[2024-01-24 12:09:33,017] [INFO] Running command: hmmsearch --tblout GCF_020685205.1_ASM2068520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/reference_markers.hmm GCF_020685205.1_ASM2068520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:33,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:33,291] [INFO] Found 6/6 markers.
[2024-01-24 12:09:33,332] [INFO] Query marker FASTA was written to GCF_020685205.1_ASM2068520v1_genomic.fna/markers.fasta
[2024-01-24 12:09:33,332] [INFO] Task started: Blastn
[2024-01-24 12:09:33,333] [INFO] Running command: blastn -query GCF_020685205.1_ASM2068520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/reference_markers.fasta -out GCF_020685205.1_ASM2068520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:33,972] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:33,976] [INFO] Selected 15 target genomes.
[2024-01-24 12:09:33,977] [INFO] Target genome list was writen to GCF_020685205.1_ASM2068520v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:33,984] [INFO] Task started: fastANI
[2024-01-24 12:09:33,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg3499494a-e5be-4ff2-ab91-233ab5a629ed/GCF_020685205.1_ASM2068520v1_genomic.fna.gz --refList GCF_020685205.1_ASM2068520v1_genomic.fna/target_genomes.txt --output GCF_020685205.1_ASM2068520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:49,613] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:49,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:49,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:49,630] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:09:49,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:09:49,630] [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 aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	81.7922	979	1639	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	81.5292	953	1639	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	81.2583	981	1639	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	80.7654	882	1639	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.6324	945	1639	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.4119	811	1639	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.3092	832	1639	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	80.2515	797	1639	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	80.1706	801	1639	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	79.9109	786	1639	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	79.5596	747	1639	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.2045	732	1639	95	below_threshold
Hymenobacter citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	78.5965	604	1639	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.4597	518	1639	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	78.1745	555	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:49,632] [INFO] DFAST Taxonomy check result was written to GCF_020685205.1_ASM2068520v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:49,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:49,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:49,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/checkm_data
[2024-01-24 12:09:49,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:49,699] [INFO] Task started: CheckM
[2024-01-24 12:09:49,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020685205.1_ASM2068520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020685205.1_ASM2068520v1_genomic.fna/checkm_input GCF_020685205.1_ASM2068520v1_genomic.fna/checkm_result
[2024-01-24 12:11:00,582] [INFO] Task succeeded: CheckM
[2024-01-24 12:11:00,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:11:00,608] [INFO] ===== Completeness check finished =====
[2024-01-24 12:11:00,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:11:00,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020685205.1_ASM2068520v1_genomic.fna/markers.fasta)
[2024-01-24 12:11:00,610] [INFO] Task started: Blastn
[2024-01-24 12:11:00,610] [INFO] Running command: blastn -query GCF_020685205.1_ASM2068520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d060d-7858-4a48-8a1f-cc6f134ca830/dqc_reference/reference_markers_gtdb.fasta -out GCF_020685205.1_ASM2068520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:11:01,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:11:01,529] [INFO] Selected 14 target genomes.
[2024-01-24 12:11:01,529] [INFO] Target genome list was writen to GCF_020685205.1_ASM2068520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:11:01,583] [INFO] Task started: fastANI
[2024-01-24 12:11:01,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg3499494a-e5be-4ff2-ab91-233ab5a629ed/GCF_020685205.1_ASM2068520v1_genomic.fna.gz --refList GCF_020685205.1_ASM2068520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020685205.1_ASM2068520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:11:16,150] [INFO] Task succeeded: fastANI
[2024-01-24 12:11:16,166] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:11:16,166] [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_004765605.1	s__Hymenobacter aquaticus	81.7982	978	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	81.5243	954	1639	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	81.2354	983	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	80.7393	886	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	80.6158	947	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	80.41	871	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	80.4089	811	1639	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	80.2672	804	1639	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	80.259	796	1639	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	80.1706	801	1639	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	79.7642	768	1639	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	79.5494	748	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352025.1	s__Hymenobacter sp006352025	79.4795	779	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337165.1	s__Hymenobacter jejuensis	78.1656	557	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:11:16,168] [INFO] GTDB search result was written to GCF_020685205.1_ASM2068520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:11:16,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:11:16,172] [INFO] DFAST_QC result json was written to GCF_020685205.1_ASM2068520v1_genomic.fna/dqc_result.json
[2024-01-24 12:11:16,172] [INFO] DFAST_QC completed!
[2024-01-24 12:11:16,172] [INFO] Total running time: 0h2m11s