[2024-01-24 14:20:14,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference
[2024-01-24 14:20:15,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,650] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg3781b941-ab0a-474c-8af8-f6dfd4714a1e/GCF_003008425.1_ASM300842v1_genomic.fna.gz | prodigal -d GCF_003008425.1_ASM300842v1_genomic.fna/cds.fna -a GCF_003008425.1_ASM300842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:24,519] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:24,519] [INFO] Task started: HMMsearch
[2024-01-24 14:20:24,520] [INFO] Running command: hmmsearch --tblout GCF_003008425.1_ASM300842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/reference_markers.hmm GCF_003008425.1_ASM300842v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:24,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:24,754] [INFO] Found 6/6 markers.
[2024-01-24 14:20:24,781] [INFO] Query marker FASTA was written to GCF_003008425.1_ASM300842v1_genomic.fna/markers.fasta
[2024-01-24 14:20:24,781] [INFO] Task started: Blastn
[2024-01-24 14:20:24,782] [INFO] Running command: blastn -query GCF_003008425.1_ASM300842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/reference_markers.fasta -out GCF_003008425.1_ASM300842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,513] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,518] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:25,518] [INFO] Target genome list was writen to GCF_003008425.1_ASM300842v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:25,540] [INFO] Task started: fastANI
[2024-01-24 14:20:25,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg3781b941-ab0a-474c-8af8-f6dfd4714a1e/GCF_003008425.1_ASM300842v1_genomic.fna.gz --refList GCF_003008425.1_ASM300842v1_genomic.fna/target_genomes.txt --output GCF_003008425.1_ASM300842v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:41,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:41,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:41,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:41,851] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:41,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:41,852] [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
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	100.0	961	964	95	conclusive
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	78.4389	284	964	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.1968	295	964	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	78.1131	297	964	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	78.0113	291	964	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.9954	291	964	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	77.9863	271	964	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.9759	311	964	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.9514	269	964	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.9271	301	964	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.783	211	964	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.7684	186	964	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.7135	245	964	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.7135	245	964	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	77.7083	205	964	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6602	242	964	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	77.6369	227	964	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.6156	195	964	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.5204	240	964	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.47	180	964	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.4587	224	964	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2782	134	964	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.1985	125	964	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.7647	108	964	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,854] [INFO] DFAST Taxonomy check result was written to GCF_003008425.1_ASM300842v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:41,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:41,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:41,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/checkm_data
[2024-01-24 14:20:41,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:41,887] [INFO] Task started: CheckM
[2024-01-24 14:20:41,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003008425.1_ASM300842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003008425.1_ASM300842v1_genomic.fna/checkm_input GCF_003008425.1_ASM300842v1_genomic.fna/checkm_result
[2024-01-24 14:21:10,584] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:10,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:10,608] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:10,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:10,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003008425.1_ASM300842v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:10,609] [INFO] Task started: Blastn
[2024-01-24 14:21:10,610] [INFO] Running command: blastn -query GCF_003008425.1_ASM300842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg649b695e-eb94-431f-b750-6ac309ba7c05/dqc_reference/reference_markers_gtdb.fasta -out GCF_003008425.1_ASM300842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:11,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:11,537] [INFO] Selected 22 target genomes.
[2024-01-24 14:21:11,537] [INFO] Target genome list was writen to GCF_003008425.1_ASM300842v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:11,567] [INFO] Task started: fastANI
[2024-01-24 14:21:11,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg3781b941-ab0a-474c-8af8-f6dfd4714a1e/GCF_003008425.1_ASM300842v1_genomic.fna.gz --refList GCF_003008425.1_ASM300842v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003008425.1_ASM300842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:25,230] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:25,247] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:25,247] [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_003008425.1	s__Aurantibacter aestuarii	100.0	960	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259525.1	s__Olleya aquimaris	78.4246	285	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004843725.1	s__Olleya sp004843725	78.3258	264	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211855.2	s__Lacinutrix sp000211855	78.2862	342	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.1642	305	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_014764305.1	s__Mesoflavibacter profundi	78.1523	297	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_007827365.1	s__Olleya sp002323495	78.1351	296	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.1329	317	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831665.1	s__Lacinutrix sp002831665	78.0746	301	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.0128	216	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	77.9781	312	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_900114005.1	s__Olleya namhaensis	77.9737	272	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.9626	293	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.9271	301	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	77.9165	309	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_008806375.1	s__Tamlana_A haliotis	77.8029	187	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.665	242	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	77.6609	210	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.6158	208	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_007197735.1	s__Formosa sediminum	77.6054	228	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.5241	241	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067115.1	s__Bizionia sp018067115	77.3533	178	964	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:25,249] [INFO] GTDB search result was written to GCF_003008425.1_ASM300842v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:25,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:25,254] [INFO] DFAST_QC result json was written to GCF_003008425.1_ASM300842v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:25,254] [INFO] DFAST_QC completed!
[2024-01-24 14:21:25,254] [INFO] Total running time: 0h1m11s