[2023-06-28 10:27:02,379] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:27:02,381] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:27:02,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference
[2023-06-28 10:27:05,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:27:05,711] [INFO] Task started: Prodigal
[2023-06-28 10:27:05,711] [INFO] Running command: gunzip -c /var/lib/cwl/stga1fc0c34-0003-41f3-980f-a49d52a68af4/GCA_020441165.1_ASM2044116v1_genomic.fna.gz | prodigal -d GCA_020441165.1_ASM2044116v1_genomic.fna/cds.fna -a GCA_020441165.1_ASM2044116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:27:14,697] [INFO] Task succeeded: Prodigal
[2023-06-28 10:27:14,697] [INFO] Task started: HMMsearch
[2023-06-28 10:27:14,697] [INFO] Running command: hmmsearch --tblout GCA_020441165.1_ASM2044116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/reference_markers.hmm GCA_020441165.1_ASM2044116v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:27:14,956] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:27:14,958] [INFO] Found 6/6 markers.
[2023-06-28 10:27:15,000] [INFO] Query marker FASTA was written to GCA_020441165.1_ASM2044116v1_genomic.fna/markers.fasta
[2023-06-28 10:27:15,000] [INFO] Task started: Blastn
[2023-06-28 10:27:15,001] [INFO] Running command: blastn -query GCA_020441165.1_ASM2044116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/reference_markers.fasta -out GCA_020441165.1_ASM2044116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:27:15,765] [INFO] Task succeeded: Blastn
[2023-06-28 10:27:15,770] [INFO] Selected 25 target genomes.
[2023-06-28 10:27:15,770] [INFO] Target genome list was writen to GCA_020441165.1_ASM2044116v1_genomic.fna/target_genomes.txt
[2023-06-28 10:27:15,772] [INFO] Task started: fastANI
[2023-06-28 10:27:15,772] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fc0c34-0003-41f3-980f-a49d52a68af4/GCA_020441165.1_ASM2044116v1_genomic.fna.gz --refList GCA_020441165.1_ASM2044116v1_genomic.fna/target_genomes.txt --output GCA_020441165.1_ASM2044116v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:27:35,007] [INFO] Task succeeded: fastANI
[2023-06-28 10:27:35,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:27:35,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:27:35,038] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:27:35,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:27:35,039] [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
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	81.0446	521	942	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.9393	540	942	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.7035	547	942	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.6389	508	942	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.5709	476	942	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.3957	466	942	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.3602	470	942	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.9546	462	942	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.9255	448	942	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.8687	456	942	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.6855	385	942	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.6204	413	942	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.4594	403	942	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.3873	362	942	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.191	344	942	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.0166	387	942	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0068	326	942	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.8541	349	942	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.8432	359	942	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.8262	363	942	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.7279	328	942	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6216	308	942	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.433	246	942	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0826	288	942	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	77.0093	373	942	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:27:35,041] [INFO] DFAST Taxonomy check result was written to GCA_020441165.1_ASM2044116v1_genomic.fna/tc_result.tsv
[2023-06-28 10:27:35,042] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:27:35,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:27:35,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/checkm_data
[2023-06-28 10:27:35,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:27:35,090] [INFO] Task started: CheckM
[2023-06-28 10:27:35,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020441165.1_ASM2044116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020441165.1_ASM2044116v1_genomic.fna/checkm_input GCA_020441165.1_ASM2044116v1_genomic.fna/checkm_result
[2023-06-28 10:28:05,251] [INFO] Task succeeded: CheckM
[2023-06-28 10:28:05,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.04%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:28:05,281] [INFO] ===== Completeness check finished =====
[2023-06-28 10:28:05,281] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:28:05,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020441165.1_ASM2044116v1_genomic.fna/markers.fasta)
[2023-06-28 10:28:05,282] [INFO] Task started: Blastn
[2023-06-28 10:28:05,282] [INFO] Running command: blastn -query GCA_020441165.1_ASM2044116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg097e9027-984f-4563-a4b5-09415ed664f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_020441165.1_ASM2044116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:28:06,512] [INFO] Task succeeded: Blastn
[2023-06-28 10:28:06,518] [INFO] Selected 30 target genomes.
[2023-06-28 10:28:06,518] [INFO] Target genome list was writen to GCA_020441165.1_ASM2044116v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:28:06,541] [INFO] Task started: fastANI
[2023-06-28 10:28:06,541] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fc0c34-0003-41f3-980f-a49d52a68af4/GCA_020441165.1_ASM2044116v1_genomic.fna.gz --refList GCA_020441165.1_ASM2044116v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020441165.1_ASM2044116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:28:29,795] [INFO] Task succeeded: fastANI
[2023-06-28 10:28:29,819] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:28:29,819] [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_900109035.1	s__Cribrihabitans marinus	80.9586	538	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	80.6864	549	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	80.559	542	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	80.537	389	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.3564	451	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	80.3306	528	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.7492	363	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	79.7083	484	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.6361	509	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_005938215.1	s__Ruegeria sediminis	79.54	479	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.515	494	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.3952	426	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900101475.1	s__Ruegeria_B marina	79.3805	468	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	79.2593	474	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.0192	444	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.9503	463	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.9477	492	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_000442255.1	s__Salipiger mucosus	78.9068	455	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	78.8689	455	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_008086115.1	s__Muriiphilus fusiformis	78.8219	394	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	-
GCF_000473225.1	s__Sedimentitalea nanhaiensis	78.8052	439	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521865.1	s__Roseivivax isoporae	78.6235	412	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	78.5503	340	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.2315	330	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004146235.1	s__Tropicimonas sp004146235	78.1913	340	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.0562	379	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.0266	385	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016758075.1	s__CAU-1492 sp016758075	77.8591	346	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	99.98	99.98	0.95	0.95	2	-
GCF_900110425.1	s__Salinihabitans flavidus	77.8555	348	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	77.0453	369	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:28:29,822] [INFO] GTDB search result was written to GCA_020441165.1_ASM2044116v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:28:29,822] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:28:29,828] [INFO] DFAST_QC result json was written to GCA_020441165.1_ASM2044116v1_genomic.fna/dqc_result.json
[2023-06-28 10:28:29,828] [INFO] DFAST_QC completed!
[2023-06-28 10:28:29,828] [INFO] Total running time: 0h1m27s