[2024-01-24 12:23:03,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference
[2024-01-24 12:23:04,733] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,734] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,734] [INFO] Running command: gunzip -c /var/lib/cwl/stg82a8a7b3-bb26-4650-ab27-746c55885426/GCF_004346845.1_ASM434684v1_genomic.fna.gz | prodigal -d GCF_004346845.1_ASM434684v1_genomic.fna/cds.fna -a GCF_004346845.1_ASM434684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:14,442] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:14,443] [INFO] Task started: HMMsearch
[2024-01-24 12:23:14,443] [INFO] Running command: hmmsearch --tblout GCF_004346845.1_ASM434684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/reference_markers.hmm GCF_004346845.1_ASM434684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:14,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:14,656] [INFO] Found 6/6 markers.
[2024-01-24 12:23:14,682] [INFO] Query marker FASTA was written to GCF_004346845.1_ASM434684v1_genomic.fna/markers.fasta
[2024-01-24 12:23:14,682] [INFO] Task started: Blastn
[2024-01-24 12:23:14,683] [INFO] Running command: blastn -query GCF_004346845.1_ASM434684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/reference_markers.fasta -out GCF_004346845.1_ASM434684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,322] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,325] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:15,325] [INFO] Target genome list was writen to GCF_004346845.1_ASM434684v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:15,334] [INFO] Task started: fastANI
[2024-01-24 12:23:15,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a8a7b3-bb26-4650-ab27-746c55885426/GCF_004346845.1_ASM434684v1_genomic.fna.gz --refList GCF_004346845.1_ASM434684v1_genomic.fna/target_genomes.txt --output GCF_004346845.1_ASM434684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:29,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:29,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:29,251] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:29,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:29,252] [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
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	100.0	978	978	95	conclusive
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	87.9317	764	978	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	79.6046	514	978	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.089	292	978	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.9326	350	978	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.9257	350	978	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.8695	295	978	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.8502	317	978	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.8368	293	978	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.8189	285	978	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.7648	316	978	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.7567	264	978	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.4005	155	978	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.3846	131	978	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.294	121	978	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.283	199	978	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.248	230	978	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.2273	195	978	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2146	152	978	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.1288	176	978	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0939	191	978	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	77.0825	174	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,253] [INFO] DFAST Taxonomy check result was written to GCF_004346845.1_ASM434684v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:29,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:29,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:29,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/checkm_data
[2024-01-24 12:23:29,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:29,283] [INFO] Task started: CheckM
[2024-01-24 12:23:29,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346845.1_ASM434684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346845.1_ASM434684v1_genomic.fna/checkm_input GCF_004346845.1_ASM434684v1_genomic.fna/checkm_result
[2024-01-24 12:24:00,037] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:00,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,060] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:00,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:00,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346845.1_ASM434684v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:00,061] [INFO] Task started: Blastn
[2024-01-24 12:24:00,061] [INFO] Running command: blastn -query GCF_004346845.1_ASM434684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820157ad-3020-4749-8d66-a3b06697fb17/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346845.1_ASM434684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:00,907] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:00,910] [INFO] Selected 9 target genomes.
[2024-01-24 12:24:00,911] [INFO] Target genome list was writen to GCF_004346845.1_ASM434684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:00,917] [INFO] Task started: fastANI
[2024-01-24 12:24:00,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a8a7b3-bb26-4650-ab27-746c55885426/GCF_004346845.1_ASM434684v1_genomic.fna.gz --refList GCF_004346845.1_ASM434684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346845.1_ASM434684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:06,146] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:06,154] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:06,155] [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_004346845.1	s__Winogradskyella wandonensis	100.0	978	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129745.1	s__Winogradskyella jejuensis	87.9215	765	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	79.6012	513	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211785.1	s__Winogradskyella sp004211785	79.2371	459	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	79.1916	414	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_002163855.1	s__Winogradskyella sp002163855	79.0646	514	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_905480385.1	s__Winogradskyella sp905480385	78.6941	377	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCF_014297365.1	s__Winogradskyella echinorum	77.9212	351	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013002225.1	s__Winogradskyella sp013002225	77.2326	215	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 12:24:06,156] [INFO] GTDB search result was written to GCF_004346845.1_ASM434684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:06,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:06,162] [INFO] DFAST_QC result json was written to GCF_004346845.1_ASM434684v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:06,162] [INFO] DFAST_QC completed!
[2024-01-24 12:24:06,162] [INFO] Total running time: 0h1m3s