[2024-01-24 13:13:03,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:03,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:03,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference
[2024-01-24 13:13:04,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,231] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,231] [INFO] Running command: gunzip -c /var/lib/cwl/stga77d59f6-d052-4581-946c-96143d09b4d5/GCF_003208435.1_ASM320843v1_genomic.fna.gz | prodigal -d GCF_003208435.1_ASM320843v1_genomic.fna/cds.fna -a GCF_003208435.1_ASM320843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:20,643] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:20,643] [INFO] Task started: HMMsearch
[2024-01-24 13:13:20,644] [INFO] Running command: hmmsearch --tblout GCF_003208435.1_ASM320843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/reference_markers.hmm GCF_003208435.1_ASM320843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:20,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:20,931] [INFO] Found 6/6 markers.
[2024-01-24 13:13:20,978] [INFO] Query marker FASTA was written to GCF_003208435.1_ASM320843v1_genomic.fna/markers.fasta
[2024-01-24 13:13:20,979] [INFO] Task started: Blastn
[2024-01-24 13:13:20,979] [INFO] Running command: blastn -query GCF_003208435.1_ASM320843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/reference_markers.fasta -out GCF_003208435.1_ASM320843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:21,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:21,632] [INFO] Selected 25 target genomes.
[2024-01-24 13:13:21,632] [INFO] Target genome list was writen to GCF_003208435.1_ASM320843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,692] [INFO] Task started: fastANI
[2024-01-24 13:13:21,692] [INFO] Running command: fastANI --query /var/lib/cwl/stga77d59f6-d052-4581-946c-96143d09b4d5/GCF_003208435.1_ASM320843v1_genomic.fna.gz --refList GCF_003208435.1_ASM320843v1_genomic.fna/target_genomes.txt --output GCF_003208435.1_ASM320843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:38,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:38,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:38,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:38,884] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:38,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:38,884] [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
Pelagimonas varians	strain=DSM 23678	GCA_003208435.1	696760	696760	type	True	100.0	1610	1615	95	conclusive
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	78.4587	559	1615	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.2164	147	1615	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	77.0631	125	1615	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	77.021	212	1615	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	77.0201	152	1615	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.9842	174	1615	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.904	181	1615	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	76.9006	148	1615	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.8817	241	1615	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8568	177	1615	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.6989	202	1615	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6743	168	1615	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.6418	134	1615	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	76.6418	160	1615	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.6227	191	1615	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	76.5793	158	1615	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.4656	153	1615	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	76.4582	128	1615	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	76.3446	122	1615	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.3275	102	1615	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2702	125	1615	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	76.1736	62	1615	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	76.1236	93	1615	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	76.0911	80	1615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,886] [INFO] DFAST Taxonomy check result was written to GCF_003208435.1_ASM320843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:38,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:38,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:38,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/checkm_data
[2024-01-24 13:13:38,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:38,940] [INFO] Task started: CheckM
[2024-01-24 13:13:38,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003208435.1_ASM320843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003208435.1_ASM320843v1_genomic.fna/checkm_input GCF_003208435.1_ASM320843v1_genomic.fna/checkm_result
[2024-01-24 13:14:29,747] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:29,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,771] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:29,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:29,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003208435.1_ASM320843v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:29,772] [INFO] Task started: Blastn
[2024-01-24 13:14:29,772] [INFO] Running command: blastn -query GCF_003208435.1_ASM320843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74b55f83-6754-49a8-865c-de08c215c500/dqc_reference/reference_markers_gtdb.fasta -out GCF_003208435.1_ASM320843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:30,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:30,692] [INFO] Selected 21 target genomes.
[2024-01-24 13:14:30,693] [INFO] Target genome list was writen to GCF_003208435.1_ASM320843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:30,743] [INFO] Task started: fastANI
[2024-01-24 13:14:30,744] [INFO] Running command: fastANI --query /var/lib/cwl/stga77d59f6-d052-4581-946c-96143d09b4d5/GCF_003208435.1_ASM320843v1_genomic.fna.gz --refList GCF_003208435.1_ASM320843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003208435.1_ASM320843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:45,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:45,391] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:45,392] [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_003208435.1	s__Pelagimonas varians	100.0	1610	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_004364805.1	s__Pelagimonas phthalicica	78.4587	559	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCF_900112755.1	s__Sulfitobacter brevis	77.2164	147	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	77.2136	313	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004804335.1	s__Pelagimonas sp004804335	77.0764	253	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108225.1	s__Thalassococcus halodurans	77.0331	211	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	-
GCF_009617595.1	s__Epibacterium aquimaris	77.016	153	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302455.1	s__Ruegeria_E mediterranea	76.9842	174	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_900114415.1	s__Shimia haliotis	76.904	181	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	76.8587	270	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	76.7962	142	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.7518	87	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	76.6994	201	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	76.6991	188	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205515.1	s__Litorivita pollutaquae	76.6418	160	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorivita	95.0	98.23	98.23	0.93	0.93	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.4779	152	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	76.3513	148	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.2067	153	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	76.0956	75	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	76.0857	76	1615	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:45,393] [INFO] GTDB search result was written to GCF_003208435.1_ASM320843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:45,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:45,398] [INFO] DFAST_QC result json was written to GCF_003208435.1_ASM320843v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:45,399] [INFO] DFAST_QC completed!
[2024-01-24 13:14:45,399] [INFO] Total running time: 0h1m42s