[2024-01-24 13:49:40,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,043] [INFO] DQC Reference Directory: /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference
[2024-01-24 13:49:41,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,120] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fdf7eaa-558c-47e0-b7ec-38c48d4afe79/GCF_004803475.1_ASM480347v1_genomic.fna.gz | prodigal -d GCF_004803475.1_ASM480347v1_genomic.fna/cds.fna -a GCF_004803475.1_ASM480347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:55,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:55,307] [INFO] Task started: HMMsearch
[2024-01-24 13:49:55,307] [INFO] Running command: hmmsearch --tblout GCF_004803475.1_ASM480347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/reference_markers.hmm GCF_004803475.1_ASM480347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:55,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:55,509] [INFO] Found 6/6 markers.
[2024-01-24 13:49:55,541] [INFO] Query marker FASTA was written to GCF_004803475.1_ASM480347v1_genomic.fna/markers.fasta
[2024-01-24 13:49:55,541] [INFO] Task started: Blastn
[2024-01-24 13:49:55,541] [INFO] Running command: blastn -query GCF_004803475.1_ASM480347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/reference_markers.fasta -out GCF_004803475.1_ASM480347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,366] [INFO] Selected 30 target genomes.
[2024-01-24 13:49:56,367] [INFO] Target genome list was writen to GCF_004803475.1_ASM480347v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:56,371] [INFO] Task started: fastANI
[2024-01-24 13:49:56,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fdf7eaa-558c-47e0-b7ec-38c48d4afe79/GCF_004803475.1_ASM480347v1_genomic.fna.gz --refList GCF_004803475.1_ASM480347v1_genomic.fna/target_genomes.txt --output GCF_004803475.1_ASM480347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:17,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:17,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:17,648] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:17,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:17,648] [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
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	100.0	1351	1353	95	conclusive
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.1188	436	1353	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.088	445	1353	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.9743	384	1353	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.9534	378	1353	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.8154	407	1353	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.8046	414	1353	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.7886	388	1353	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.7764	437	1353	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.7654	463	1353	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.7031	330	1353	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.7018	408	1353	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.6936	366	1353	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.6926	332	1353	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.6582	372	1353	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6357	408	1353	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.5155	352	1353	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.5127	331	1353	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.4826	322	1353	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.4411	297	1353	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.4309	298	1353	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.4156	328	1353	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.4108	314	1353	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.4081	294	1353	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.2099	322	1353	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.1573	307	1353	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.1314	272	1353	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.1216	273	1353	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.1191	255	1353	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	76.9312	208	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,650] [INFO] DFAST Taxonomy check result was written to GCF_004803475.1_ASM480347v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:17,650] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:17,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:17,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/checkm_data
[2024-01-24 13:50:17,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:17,692] [INFO] Task started: CheckM
[2024-01-24 13:50:17,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004803475.1_ASM480347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004803475.1_ASM480347v1_genomic.fna/checkm_input GCF_004803475.1_ASM480347v1_genomic.fna/checkm_result
[2024-01-24 13:50:55,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:55,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:55,401] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:55,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:55,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004803475.1_ASM480347v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:55,401] [INFO] Task started: Blastn
[2024-01-24 13:50:55,401] [INFO] Running command: blastn -query GCF_004803475.1_ASM480347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce35cc48-630e-43d0-a9c7-ed38f51cc8e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004803475.1_ASM480347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:56,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:56,909] [INFO] Selected 27 target genomes.
[2024-01-24 13:50:56,909] [INFO] Target genome list was writen to GCF_004803475.1_ASM480347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:56,923] [INFO] Task started: fastANI
[2024-01-24 13:50:56,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fdf7eaa-558c-47e0-b7ec-38c48d4afe79/GCF_004803475.1_ASM480347v1_genomic.fna.gz --refList GCF_004803475.1_ASM480347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004803475.1_ASM480347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:18,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:18,155] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:18,155] [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_004803475.1	s__Aliishimia ponticola	100.0	1351	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013030985.1	s__Ruegeria arenilitoris_B	77.8075	366	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.7766	437	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.7754	437	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_001679925.1	s__Leisingera sp001679925	77.7667	366	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	77.7582	463	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.7504	340	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.7429	352	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.733	433	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	77.7092	359	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	77.7076	406	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_002115805.1	s__Marivita geojedonensis	77.6921	332	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900101475.1	s__Ruegeria_B marina	77.689	389	1353	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_009363555.1	s__Sulfitobacter sp009363555	77.6717	423	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	77.6585	377	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	77.6529	379	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.6465	440	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.627	379	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.5129	331	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	77.5065	353	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	77.506	254	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.4758	322	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015223355.1	s__Salipiger pacificus_B	77.4233	317	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	77.3224	319	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900110425.1	s__Salinihabitans flavidus	77.2637	316	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.2186	273	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350345.1	s__Rhodobaculum breve	76.9313	208	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:18,156] [INFO] GTDB search result was written to GCF_004803475.1_ASM480347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:18,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:18,161] [INFO] DFAST_QC result json was written to GCF_004803475.1_ASM480347v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:18,161] [INFO] DFAST_QC completed!
[2024-01-24 13:51:18,161] [INFO] Total running time: 0h1m38s