[2023-06-16 20:34:50,041] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:34:50,048] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:34:50,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference
[2023-06-16 20:34:51,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:34:51,398] [INFO] Task started: Prodigal
[2023-06-16 20:34:51,398] [INFO] Running command: gunzip -c /var/lib/cwl/stgd48e880e-dd8d-4da4-907c-e88267d5dbf0/GCA_009693635.1_ASM969363v1_genomic.fna.gz | prodigal -d GCA_009693635.1_ASM969363v1_genomic.fna/cds.fna -a GCA_009693635.1_ASM969363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:34:57,435] [INFO] Task succeeded: Prodigal
[2023-06-16 20:34:57,436] [INFO] Task started: HMMsearch
[2023-06-16 20:34:57,436] [INFO] Running command: hmmsearch --tblout GCA_009693635.1_ASM969363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/reference_markers.hmm GCA_009693635.1_ASM969363v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:34:57,631] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:34:57,632] [INFO] Found 6/6 markers.
[2023-06-16 20:34:57,656] [INFO] Query marker FASTA was written to GCA_009693635.1_ASM969363v1_genomic.fna/markers.fasta
[2023-06-16 20:34:57,656] [INFO] Task started: Blastn
[2023-06-16 20:34:57,656] [INFO] Running command: blastn -query GCA_009693635.1_ASM969363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/reference_markers.fasta -out GCA_009693635.1_ASM969363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:34:58,334] [INFO] Task succeeded: Blastn
[2023-06-16 20:34:58,339] [INFO] Selected 27 target genomes.
[2023-06-16 20:34:58,339] [INFO] Target genome list was writen to GCA_009693635.1_ASM969363v1_genomic.fna/target_genomes.txt
[2023-06-16 20:34:58,347] [INFO] Task started: fastANI
[2023-06-16 20:34:58,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48e880e-dd8d-4da4-907c-e88267d5dbf0/GCA_009693635.1_ASM969363v1_genomic.fna.gz --refList GCA_009693635.1_ASM969363v1_genomic.fna/target_genomes.txt --output GCA_009693635.1_ASM969363v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:35:14,515] [INFO] Task succeeded: fastANI
[2023-06-16 20:35:14,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:35:14,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:35:14,535] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:35:14,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:35:14,536] [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
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	78.5395	233	559	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	78.488	216	559	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	78.3186	216	559	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	78.3169	215	559	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.2987	215	559	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	78.2503	233	559	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	78.233	209	559	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	78.1918	220	559	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.1755	210	559	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.1213	186	559	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	78.0892	200	559	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	78.0137	184	559	95	below_threshold
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	78.0026	206	559	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	77.9815	192	559	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	77.9116	224	559	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	77.9083	189	559	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.8916	233	559	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	77.8595	202	559	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	77.8214	217	559	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	77.786	187	559	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	77.7478	177	559	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	77.7406	191	559	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	77.6332	200	559	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	77.6069	180	559	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.5067	161	559	95	below_threshold
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	76.9204	128	559	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.6322	137	559	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:35:14,540] [INFO] DFAST Taxonomy check result was written to GCA_009693635.1_ASM969363v1_genomic.fna/tc_result.tsv
[2023-06-16 20:35:14,540] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:35:14,541] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:35:14,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/checkm_data
[2023-06-16 20:35:14,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:35:14,563] [INFO] Task started: CheckM
[2023-06-16 20:35:14,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009693635.1_ASM969363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009693635.1_ASM969363v1_genomic.fna/checkm_input GCA_009693635.1_ASM969363v1_genomic.fna/checkm_result
[2023-06-16 20:35:38,296] [INFO] Task succeeded: CheckM
[2023-06-16 20:35:38,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 20:35:38,322] [INFO] ===== Completeness check finished =====
[2023-06-16 20:35:38,322] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:35:38,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009693635.1_ASM969363v1_genomic.fna/markers.fasta)
[2023-06-16 20:35:38,323] [INFO] Task started: Blastn
[2023-06-16 20:35:38,323] [INFO] Running command: blastn -query GCA_009693635.1_ASM969363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9453044-6603-4fbb-ab9b-c55dbb2928e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_009693635.1_ASM969363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:35:39,288] [INFO] Task succeeded: Blastn
[2023-06-16 20:35:39,291] [INFO] Selected 13 target genomes.
[2023-06-16 20:35:39,292] [INFO] Target genome list was writen to GCA_009693635.1_ASM969363v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:35:39,305] [INFO] Task started: fastANI
[2023-06-16 20:35:39,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgd48e880e-dd8d-4da4-907c-e88267d5dbf0/GCA_009693635.1_ASM969363v1_genomic.fna.gz --refList GCA_009693635.1_ASM969363v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009693635.1_ASM969363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:35:45,824] [INFO] Task succeeded: fastANI
[2023-06-16 20:35:45,836] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:35:45,837] [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
GCA_009693635.1	s__Flavobacterium sp009693635	99.9999	554	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903819815.1	s__Flavobacterium sp903819815	82.6468	321	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000439025.2	s__Flavobacterium sp000439025	81.4155	361	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926065.1	s__Flavobacterium sp009926065	80.6459	369	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	78.9651	263	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCA_903824755.1	s__Flavobacterium sp903824755	78.6543	231	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	78.5075	227	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	78.0479	185	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	77.9306	229	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_900129545.1	s__Flavobacterium fluvii	77.8632	203	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	77.8319	217	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	77.7406	191	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920835.1	s__Flavobacterium sp903920835	76.6822	78	559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:35:45,839] [INFO] GTDB search result was written to GCA_009693635.1_ASM969363v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:35:45,839] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:35:45,845] [INFO] DFAST_QC result json was written to GCA_009693635.1_ASM969363v1_genomic.fna/dqc_result.json
[2023-06-16 20:35:45,845] [INFO] DFAST_QC completed!
[2023-06-16 20:35:45,845] [INFO] Total running time: 0h0m56s