[2024-01-24 14:19:34,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:34,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:34,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference
[2024-01-24 14:19:35,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:35,856] [INFO] Task started: Prodigal
[2024-01-24 14:19:35,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg28ffa2b7-34ce-4b28-bd0b-812d1cb8aac3/GCF_002954355.1_ASM295435v1_genomic.fna.gz | prodigal -d GCF_002954355.1_ASM295435v1_genomic.fna/cds.fna -a GCF_002954355.1_ASM295435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:46,751] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:46,751] [INFO] Task started: HMMsearch
[2024-01-24 14:19:46,751] [INFO] Running command: hmmsearch --tblout GCF_002954355.1_ASM295435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/reference_markers.hmm GCF_002954355.1_ASM295435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:47,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:47,034] [INFO] Found 6/6 markers.
[2024-01-24 14:19:47,267] [INFO] Query marker FASTA was written to GCF_002954355.1_ASM295435v1_genomic.fna/markers.fasta
[2024-01-24 14:19:47,267] [INFO] Task started: Blastn
[2024-01-24 14:19:47,267] [INFO] Running command: blastn -query GCF_002954355.1_ASM295435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/reference_markers.fasta -out GCF_002954355.1_ASM295435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:47,940] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:47,944] [INFO] Selected 18 target genomes.
[2024-01-24 14:19:47,944] [INFO] Target genome list was writen to GCF_002954355.1_ASM295435v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:47,984] [INFO] Task started: fastANI
[2024-01-24 14:19:47,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ffa2b7-34ce-4b28-bd0b-812d1cb8aac3/GCF_002954355.1_ASM295435v1_genomic.fna.gz --refList GCF_002954355.1_ASM295435v1_genomic.fna/target_genomes.txt --output GCF_002954355.1_ASM295435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:59,972] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:59,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:59,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:59,985] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:59,986] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:59,986] [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
Nonlabens tegetincola	strain=JCM 12886	GCA_002954355.1	323273	323273	type	True	100.0	989	999	95	conclusive
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	78.1772	207	999	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	78.0965	206	999	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	78.0588	206	999	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.0534	59	999	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	77.6651	212	999	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	77.2216	199	999	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	77.0205	195	999	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.0099	70	999	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	76.9919	206	999	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.9881	67	999	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.7957	72	999	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.5514	66	999	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	75.9872	65	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:59,988] [INFO] DFAST Taxonomy check result was written to GCF_002954355.1_ASM295435v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:59,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:59,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:59,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/checkm_data
[2024-01-24 14:19:59,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:00,032] [INFO] Task started: CheckM
[2024-01-24 14:20:00,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954355.1_ASM295435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954355.1_ASM295435v1_genomic.fna/checkm_input GCF_002954355.1_ASM295435v1_genomic.fna/checkm_result
[2024-01-24 14:20:36,602] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:36,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.59%
Strain heterogeneity: 76.47%
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,627] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:36,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:36,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954355.1_ASM295435v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:36,628] [INFO] Task started: Blastn
[2024-01-24 14:20:36,628] [INFO] Running command: blastn -query GCF_002954355.1_ASM295435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6eb131-08d8-4342-bbea-a18b6dfa2283/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954355.1_ASM295435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:37,735] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:37,740] [INFO] Selected 20 target genomes.
[2024-01-24 14:20:37,740] [INFO] Target genome list was writen to GCF_002954355.1_ASM295435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:37,768] [INFO] Task started: fastANI
[2024-01-24 14:20:37,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ffa2b7-34ce-4b28-bd0b-812d1cb8aac3/GCF_002954355.1_ASM295435v1_genomic.fna.gz --refList GCF_002954355.1_ASM295435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954355.1_ASM295435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:50,150] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:50,165] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:50,166] [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_002954355.1	s__Nonlabens tegetincola	100.0	989	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.69	97.39	0.93	0.90	5	conclusive
GCF_002954765.1	s__Nonlabens arenilitoris	78.0955	204	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	78.06	206	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012974865.1	s__Nonlabens sp012974865	77.6111	174	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101765.1	s__Nonlabens sp900101765	77.5207	123	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831625.1	s__Nonlabens sp002831625	77.4892	164	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153385.1	s__Nonlabens sp000153385	77.3739	198	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732625.1	s__Nonlabens ulvanivorans	77.2216	199	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	98.59	98.07	0.92	0.89	5	-
GCF_000755285.1	s__Nonlabens ulvanivorans_A	77.0457	198	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	-
GCF_002934445.1	s__Nonlabens xylanidelens	77.004	205	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018401815.1	s__Nonlabens sp018401815	76.9643	144	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	76.9398	167	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	76.5734	65	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	76.4833	66	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	76.4202	69	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_900112245.1	s__Maribacter stanieri	76.1775	54	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001418085.1	s__Lacinutrix algicola	76.1409	69	999	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,167] [INFO] GTDB search result was written to GCF_002954355.1_ASM295435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:50,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:50,172] [INFO] DFAST_QC result json was written to GCF_002954355.1_ASM295435v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:50,173] [INFO] DFAST_QC completed!
[2024-01-24 14:20:50,173] [INFO] Total running time: 0h1m16s