[2024-01-24 15:10:49,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:49,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:49,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference
[2024-01-24 15:10:51,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,129] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg6de1d20a-92ad-4f4d-ab4b-4dcc02698842/GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/cds.fna -a GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:05,598] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:05,598] [INFO] Task started: HMMsearch
[2024-01-24 15:11:05,598] [INFO] Running command: hmmsearch --tblout GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/reference_markers.hmm GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:05,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:05,915] [INFO] Found 6/6 markers.
[2024-01-24 15:11:05,955] [INFO] Query marker FASTA was written to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:11:05,956] [INFO] Task started: Blastn
[2024-01-24 15:11:05,956] [INFO] Running command: blastn -query GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/reference_markers.fasta -out GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,657] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,663] [INFO] Selected 24 target genomes.
[2024-01-24 15:11:06,663] [INFO] Target genome list was writen to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:11:06,672] [INFO] Task started: fastANI
[2024-01-24 15:11:06,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de1d20a-92ad-4f4d-ab4b-4dcc02698842/GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna.gz --refList GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:25,924] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:25,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:25,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:25,942] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:25,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:25,942] [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
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	100.0	1287	1288	95	conclusive
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	79.6404	542	1288	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	77.8699	78	1288	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	77.3875	84	1288	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.9976	64	1288	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.8738	108	1288	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.8629	145	1288	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	76.7906	86	1288	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.7162	106	1288	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.6635	75	1288	95	below_threshold
Imtechella halotolerans	strain=K1	GCA_000260835.1	1165090	1165090	type	True	76.6195	99	1288	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.5597	65	1288	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.5456	72	1288	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.5051	65	1288	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.4823	63	1288	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.3757	68	1288	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.3324	75	1288	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.3281	71	1288	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3241	72	1288	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	76.2933	93	1288	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.1564	68	1288	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.1168	77	1288	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	75.9199	62	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:25,944] [INFO] DFAST Taxonomy check result was written to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:25,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:25,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:25,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/checkm_data
[2024-01-24 15:11:25,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:25,990] [INFO] Task started: CheckM
[2024-01-24 15:11:25,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/checkm_input GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:12:11,303] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:11,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:11,326] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:11,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:11,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:12:11,327] [INFO] Task started: Blastn
[2024-01-24 15:12:11,327] [INFO] Running command: blastn -query GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ae0b94-4bd6-436b-91de-4184d41f737f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:12,234] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:12,238] [INFO] Selected 28 target genomes.
[2024-01-24 15:12:12,238] [INFO] Target genome list was writen to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:12,258] [INFO] Task started: fastANI
[2024-01-24 15:12:12,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de1d20a-92ad-4f4d-ab4b-4dcc02698842/GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna.gz --refList GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:29,594] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:29,618] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:29,619] [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_900116365.1	s__Zhouia amylolytica	100.0	1287	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zhouia	95.0	98.62	98.62	0.95	0.95	2	conclusive
GCF_000300875.1	s__Galbibacter_B marinus	77.8699	78	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	77.4115	83	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.175	90	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	77.118	107	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.9763	63	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	76.8738	108	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.7672	102	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	76.7562	85	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCA_002428965.1	s__Jejuia sp002428965	76.6691	58	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	76.6285	68	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.6232	80	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260835.1	s__Imtechella halotolerans	76.6195	99	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Imtechella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.5123	56	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_014235875.1	s__Croceivirga lutea	76.5049	68	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011927795.1	s__Saonia flava	76.4788	60	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	76.455	64	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	76.4524	62	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.4352	88	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005315.1	s__Kordia jejudonensis	76.4142	76	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	76.3757	68	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	76.3501	78	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.3053	74	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	76.2798	70	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.2319	57	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	76.0914	98	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008692195.1	s__Mesonia sp008692195	76.0874	66	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:29,625] [INFO] GTDB search result was written to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:29,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:29,631] [INFO] DFAST_QC result json was written to GCF_900116365.1_IMG-taxon_2619618939_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:12:29,632] [INFO] DFAST_QC completed!
[2024-01-24 15:12:29,632] [INFO] Total running time: 0h1m40s