[2024-01-24 11:51:24,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference
[2024-01-24 11:51:26,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,227] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,227] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b739867-674e-4e6d-9090-2c7ceadb46bd/GCF_006337165.1_ASM633716v1_genomic.fna.gz | prodigal -d GCF_006337165.1_ASM633716v1_genomic.fna/cds.fna -a GCF_006337165.1_ASM633716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:56,893] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:56,893] [INFO] Task started: HMMsearch
[2024-01-24 11:51:56,893] [INFO] Running command: hmmsearch --tblout GCF_006337165.1_ASM633716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/reference_markers.hmm GCF_006337165.1_ASM633716v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:57,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:57,235] [INFO] Found 6/6 markers.
[2024-01-24 11:51:57,279] [INFO] Query marker FASTA was written to GCF_006337165.1_ASM633716v1_genomic.fna/markers.fasta
[2024-01-24 11:51:57,279] [INFO] Task started: Blastn
[2024-01-24 11:51:57,279] [INFO] Running command: blastn -query GCF_006337165.1_ASM633716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/reference_markers.fasta -out GCF_006337165.1_ASM633716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:57,944] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:57,948] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:57,949] [INFO] Target genome list was writen to GCF_006337165.1_ASM633716v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:57,957] [INFO] Task started: fastANI
[2024-01-24 11:51:57,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b739867-674e-4e6d-9090-2c7ceadb46bd/GCF_006337165.1_ASM633716v1_genomic.fna.gz --refList GCF_006337165.1_ASM633716v1_genomic.fna/target_genomes.txt --output GCF_006337165.1_ASM633716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:16,346] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:16,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:16,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:16,367] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:16,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:16,367] [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 jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	100.0	1695	1695	95	conclusive
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	78.9366	722	1695	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	78.6856	645	1695	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.5958	639	1695	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.4959	645	1695	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.4695	727	1695	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	78.3513	616	1695	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	78.155	576	1695	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	78.1072	589	1695	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	78.0732	543	1695	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.0205	561	1695	95	below_threshold
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	77.9458	527	1695	95	below_threshold
Hymenobacter citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	77.9213	576	1695	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	77.9136	557	1695	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	77.9015	559	1695	95	below_threshold
Hymenobacter sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	77.7436	513	1695	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	77.7343	533	1695	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	77.0876	374	1695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,369] [INFO] DFAST Taxonomy check result was written to GCF_006337165.1_ASM633716v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:16,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:16,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:16,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/checkm_data
[2024-01-24 11:52:16,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:16,419] [INFO] Task started: CheckM
[2024-01-24 11:52:16,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006337165.1_ASM633716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006337165.1_ASM633716v1_genomic.fna/checkm_input GCF_006337165.1_ASM633716v1_genomic.fna/checkm_result
[2024-01-24 11:53:35,269] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:35,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:35,294] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:35,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:35,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006337165.1_ASM633716v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:35,295] [INFO] Task started: Blastn
[2024-01-24 11:53:35,295] [INFO] Running command: blastn -query GCF_006337165.1_ASM633716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0440e4-84f0-4e80-b73d-1487efbb5648/dqc_reference/reference_markers_gtdb.fasta -out GCF_006337165.1_ASM633716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:36,181] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:36,185] [INFO] Selected 18 target genomes.
[2024-01-24 11:53:36,185] [INFO] Target genome list was writen to GCF_006337165.1_ASM633716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:36,197] [INFO] Task started: fastANI
[2024-01-24 11:53:36,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b739867-674e-4e6d-9090-2c7ceadb46bd/GCF_006337165.1_ASM633716v1_genomic.fna.gz --refList GCF_006337165.1_ASM633716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006337165.1_ASM633716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:53,920] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:53,937] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:53,938] [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_006337165.1	s__Hymenobacter jejuensis	100.0	1695	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	conclusive
GCF_004765605.1	s__Hymenobacter aquaticus	78.9427	721	1695	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	78.6887	645	1695	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	78.5831	642	1695	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	78.5013	644	1695	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	78.4819	647	1695	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	78.4729	727	1695	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	78.4012	623	1695	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	78.3455	617	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187375.1	s__Hymenobacter gelipurpurascens	78.1577	577	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760735.1	s__Hymenobacter sp018760735	78.0646	545	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589435.1	s__Hymenobacter defluvii	78.0047	518	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.38	96.38	0.86	0.86	2	-
GCF_014333525.1	s__Hymenobacter sp014333525	78.0002	579	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199535.1	s__Hymenobacter latericoloratus	77.9865	592	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507645.1	s__Hymenobacter sedentarius	77.9555	559	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333615.1	s__Hymenobacter citatus	77.9173	575	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003231285.1	s__Hymenobacter sediminis	77.7516	511	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	77.5972	516	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:53,939] [INFO] GTDB search result was written to GCF_006337165.1_ASM633716v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:53,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:53,944] [INFO] DFAST_QC result json was written to GCF_006337165.1_ASM633716v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:53,944] [INFO] DFAST_QC completed!
[2024-01-24 11:53:53,944] [INFO] Total running time: 0h2m29s