[2024-01-24 14:32:33,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:33,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:33,950] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference
[2024-01-24 14:32:35,351] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,352] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,352] [INFO] Running command: gunzip -c /var/lib/cwl/stga11fc70a-0b5b-4e91-82d2-bb108e0d76f4/GCF_002797755.1_ASM279775v1_genomic.fna.gz | prodigal -d GCF_002797755.1_ASM279775v1_genomic.fna/cds.fna -a GCF_002797755.1_ASM279775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:46,211] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:46,211] [INFO] Task started: HMMsearch
[2024-01-24 14:32:46,211] [INFO] Running command: hmmsearch --tblout GCF_002797755.1_ASM279775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/reference_markers.hmm GCF_002797755.1_ASM279775v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:46,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:46,485] [INFO] Found 6/6 markers.
[2024-01-24 14:32:46,517] [INFO] Query marker FASTA was written to GCF_002797755.1_ASM279775v1_genomic.fna/markers.fasta
[2024-01-24 14:32:46,518] [INFO] Task started: Blastn
[2024-01-24 14:32:46,518] [INFO] Running command: blastn -query GCF_002797755.1_ASM279775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/reference_markers.fasta -out GCF_002797755.1_ASM279775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:47,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:47,595] [INFO] Selected 25 target genomes.
[2024-01-24 14:32:47,596] [INFO] Target genome list was writen to GCF_002797755.1_ASM279775v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:47,606] [INFO] Task started: fastANI
[2024-01-24 14:32:47,607] [INFO] Running command: fastANI --query /var/lib/cwl/stga11fc70a-0b5b-4e91-82d2-bb108e0d76f4/GCF_002797755.1_ASM279775v1_genomic.fna.gz --refList GCF_002797755.1_ASM279775v1_genomic.fna/target_genomes.txt --output GCF_002797755.1_ASM279775v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:07,700] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:07,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:07,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:07,722] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:33:07,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:07,723] [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
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	100.0	1130	1131	95	conclusive
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	99.7173	904	1131	95	conclusive
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.2107	458	1131	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.1733	458	1131	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.02	399	1131	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9064	415	1131	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.8746	413	1131	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.8683	432	1131	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.8486	398	1131	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.8179	411	1131	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.8073	356	1131	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.7431	418	1131	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	78.7064	384	1131	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.6198	417	1131	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.5296	388	1131	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.4802	337	1131	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.4387	362	1131	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	78.3842	392	1131	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	78.1811	234	1131	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.1089	284	1131	95	below_threshold
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	77.9237	319	1131	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.923	249	1131	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	77.8882	293	1131	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.8351	231	1131	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.5749	277	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:07,724] [INFO] DFAST Taxonomy check result was written to GCF_002797755.1_ASM279775v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:07,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:07,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:07,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/checkm_data
[2024-01-24 14:33:07,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:07,764] [INFO] Task started: CheckM
[2024-01-24 14:33:07,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002797755.1_ASM279775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002797755.1_ASM279775v1_genomic.fna/checkm_input GCF_002797755.1_ASM279775v1_genomic.fna/checkm_result
[2024-01-24 14:33:43,083] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:43,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:43,108] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:43,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:43,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002797755.1_ASM279775v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:43,109] [INFO] Task started: Blastn
[2024-01-24 14:33:43,109] [INFO] Running command: blastn -query GCF_002797755.1_ASM279775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1bd3b2-3829-42be-af43-5d744f325f6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002797755.1_ASM279775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:45,100] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:45,105] [INFO] Selected 27 target genomes.
[2024-01-24 14:33:45,105] [INFO] Target genome list was writen to GCF_002797755.1_ASM279775v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:45,185] [INFO] Task started: fastANI
[2024-01-24 14:33:45,185] [INFO] Running command: fastANI --query /var/lib/cwl/stga11fc70a-0b5b-4e91-82d2-bb108e0d76f4/GCF_002797755.1_ASM279775v1_genomic.fna.gz --refList GCF_002797755.1_ASM279775v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002797755.1_ASM279775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:05,115] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:05,142] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:05,143] [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_002797755.1	s__Brevirhabdus pacifica	100.0	1131	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	79.9574	510	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	79.532	426	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014901205.1	s__Fluviibacterium sp014901205	79.4962	412	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.2095	472	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001650895.1	s__EhC02 sp001650895	79.1899	430	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.1733	458	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	79.057	422	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.0549	454	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	78.9742	436	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	78.9483	394	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	78.8883	324	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003072125.1	s__Roseovarius sediminicola	78.8818	395	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.7896	321	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	78.6423	415	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	78.6136	388	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.6005	293	1131	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	78.5374	398	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.4775	448	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	78.4735	337	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	78.4212	395	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	78.4038	390	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.3996	363	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.3674	386	1131	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_002285415.1	s__Actibacterium pelagium	78.1968	233	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.0374	390	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.9984	273	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:05,145] [INFO] GTDB search result was written to GCF_002797755.1_ASM279775v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:05,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:05,150] [INFO] DFAST_QC result json was written to GCF_002797755.1_ASM279775v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:05,150] [INFO] DFAST_QC completed!
[2024-01-24 14:34:05,150] [INFO] Total running time: 0h1m31s