[2024-01-24 13:12:48,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:48,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:48,278] [INFO] DQC Reference Directory: /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference
[2024-01-24 13:12:49,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:49,560] [INFO] Task started: Prodigal
[2024-01-24 13:12:49,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg32821ca3-8828-4003-bea3-e5e0a2e81222/GCF_003259525.1_ASM325952v1_genomic.fna.gz | prodigal -d GCF_003259525.1_ASM325952v1_genomic.fna/cds.fna -a GCF_003259525.1_ASM325952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:58,421] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:58,421] [INFO] Task started: HMMsearch
[2024-01-24 13:12:58,421] [INFO] Running command: hmmsearch --tblout GCF_003259525.1_ASM325952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/reference_markers.hmm GCF_003259525.1_ASM325952v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:58,711] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:58,712] [INFO] Found 6/6 markers.
[2024-01-24 13:12:58,737] [INFO] Query marker FASTA was written to GCF_003259525.1_ASM325952v1_genomic.fna/markers.fasta
[2024-01-24 13:12:58,738] [INFO] Task started: Blastn
[2024-01-24 13:12:58,738] [INFO] Running command: blastn -query GCF_003259525.1_ASM325952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/reference_markers.fasta -out GCF_003259525.1_ASM325952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:59,477] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:59,481] [INFO] Selected 17 target genomes.
[2024-01-24 13:12:59,481] [INFO] Target genome list was writen to GCF_003259525.1_ASM325952v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:59,502] [INFO] Task started: fastANI
[2024-01-24 13:12:59,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg32821ca3-8828-4003-bea3-e5e0a2e81222/GCF_003259525.1_ASM325952v1_genomic.fna.gz --refList GCF_003259525.1_ASM325952v1_genomic.fna/target_genomes.txt --output GCF_003259525.1_ASM325952v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:10,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:10,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:10,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:10,560] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:10,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:10,561] [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
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	100.0	975	978	95	conclusive
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	81.1261	679	978	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	80.7514	621	978	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	79.9425	530	978	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	79.9218	542	978	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	79.8173	539	978	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	79.5316	544	978	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	78.3092	292	978	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	78.1949	227	978	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.0449	279	978	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.0077	286	978	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.9292	275	978	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.9104	224	978	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.8256	258	978	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.5941	246	978	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.5652	231	978	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.489	203	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:10,562] [INFO] DFAST Taxonomy check result was written to GCF_003259525.1_ASM325952v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:10,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:10,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:10,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/checkm_data
[2024-01-24 13:13:10,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:10,597] [INFO] Task started: CheckM
[2024-01-24 13:13:10,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259525.1_ASM325952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259525.1_ASM325952v1_genomic.fna/checkm_input GCF_003259525.1_ASM325952v1_genomic.fna/checkm_result
[2024-01-24 13:13:41,115] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:41,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:41,147] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:41,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:41,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259525.1_ASM325952v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:41,148] [INFO] Task started: Blastn
[2024-01-24 13:13:41,148] [INFO] Running command: blastn -query GCF_003259525.1_ASM325952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga40f1fc2-38ef-43fb-9ee7-514d2a276a42/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259525.1_ASM325952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:42,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:42,163] [INFO] Selected 12 target genomes.
[2024-01-24 13:13:42,163] [INFO] Target genome list was writen to GCF_003259525.1_ASM325952v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:42,178] [INFO] Task started: fastANI
[2024-01-24 13:13:42,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg32821ca3-8828-4003-bea3-e5e0a2e81222/GCF_003259525.1_ASM325952v1_genomic.fna.gz --refList GCF_003259525.1_ASM325952v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259525.1_ASM325952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:50,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:50,819] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:50,819] [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_003259525.1	s__Olleya aquimaris	100.0	975	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000518485.1	s__Olleya marilimosa	81.1321	677	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_007827365.1	s__Olleya sp002323495	81.1176	652	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_900114005.1	s__Olleya namhaensis	80.7573	620	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_016785945.1	s__Olleya sediminilitoris	80.7331	642	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_004843725.1	s__Olleya sp004843725	80.4374	589	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	80.3209	595	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	79.9402	531	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_014764305.1	s__Mesoflavibacter profundi	79.5257	546	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_003663945.1	s__Lacinutrix venerupis	79.0025	467	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_002831665.1	s__Lacinutrix sp002831665	78.6376	482	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.3194	314	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,821] [INFO] GTDB search result was written to GCF_003259525.1_ASM325952v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:50,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:50,827] [INFO] DFAST_QC result json was written to GCF_003259525.1_ASM325952v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:50,827] [INFO] DFAST_QC completed!
[2024-01-24 13:13:50,827] [INFO] Total running time: 0h1m3s