[2024-01-25 18:11:05,772] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference
[2024-01-25 18:11:06,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,913] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg40445026-6ec1-4ac0-a6ff-b440089af753/GCF_003112435.1_ASM311243v1_genomic.fna.gz | prodigal -d GCF_003112435.1_ASM311243v1_genomic.fna/cds.fna -a GCF_003112435.1_ASM311243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:17,195] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:17,195] [INFO] Task started: HMMsearch
[2024-01-25 18:11:17,195] [INFO] Running command: hmmsearch --tblout GCF_003112435.1_ASM311243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/reference_markers.hmm GCF_003112435.1_ASM311243v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:17,452] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:17,454] [INFO] Found 6/6 markers.
[2024-01-25 18:11:17,484] [INFO] Query marker FASTA was written to GCF_003112435.1_ASM311243v1_genomic.fna/markers.fasta
[2024-01-25 18:11:17,484] [INFO] Task started: Blastn
[2024-01-25 18:11:17,485] [INFO] Running command: blastn -query GCF_003112435.1_ASM311243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/reference_markers.fasta -out GCF_003112435.1_ASM311243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:18,180] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:18,183] [INFO] Selected 32 target genomes.
[2024-01-25 18:11:18,184] [INFO] Target genome list was writen to GCF_003112435.1_ASM311243v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:18,203] [INFO] Task started: fastANI
[2024-01-25 18:11:18,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg40445026-6ec1-4ac0-a6ff-b440089af753/GCF_003112435.1_ASM311243v1_genomic.fna.gz --refList GCF_003112435.1_ASM311243v1_genomic.fna/target_genomes.txt --output GCF_003112435.1_ASM311243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:39,018] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:39,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:39,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:39,034] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:39,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:39,034] [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
Novimethylophilus kurashikiensis	strain=La2-4	GCA_003112435.1	1825523	1825523	type	True	100.0	1212	1212	95	conclusive
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.6027	158	1212	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	77.5112	140	1212	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	77.4461	137	1212	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.2003	147	1212	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	77.1983	143	1212	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	77.0663	103	1212	95	below_threshold
Cognatazoarcus halotolerans	strain=HKLI-1	GCA_009800965.1	2686016	2686016	type	True	77.0433	70	1212	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	76.9929	105	1212	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	76.9174	127	1212	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.8905	89	1212	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	76.8254	93	1212	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.7535	105	1212	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	76.6956	74	1212	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.689	110	1212	95	below_threshold
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	76.6722	91	1212	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.6694	75	1212	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.6561	116	1212	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.6227	118	1212	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.6146	105	1212	95	below_threshold
Methylobacillus methanolivorans	strain=VKM B-3037	GCA_020531845.1	1848927	1848927	type	True	76.5934	88	1212	95	below_threshold
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	76.5712	83	1212	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.4999	102	1212	95	below_threshold
Casimicrobium huifangae	strain=SJ-1	GCA_009746125.1	2591109	2591109	type	True	76.3633	64	1212	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.218	96	1212	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	76.1958	88	1212	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	76.1846	71	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:39,036] [INFO] DFAST Taxonomy check result was written to GCF_003112435.1_ASM311243v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:39,036] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:39,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:39,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/checkm_data
[2024-01-25 18:11:39,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:39,077] [INFO] Task started: CheckM
[2024-01-25 18:11:39,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003112435.1_ASM311243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003112435.1_ASM311243v1_genomic.fna/checkm_input GCF_003112435.1_ASM311243v1_genomic.fna/checkm_result
[2024-01-25 18:12:11,162] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:11,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:11,181] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:11,181] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:11,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003112435.1_ASM311243v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:11,182] [INFO] Task started: Blastn
[2024-01-25 18:12:11,182] [INFO] Running command: blastn -query GCF_003112435.1_ASM311243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f571310-b7d2-445c-84f4-fd3e2de37032/dqc_reference/reference_markers_gtdb.fasta -out GCF_003112435.1_ASM311243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:12,402] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:12,405] [INFO] Selected 32 target genomes.
[2024-01-25 18:12:12,405] [INFO] Target genome list was writen to GCF_003112435.1_ASM311243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:12,452] [INFO] Task started: fastANI
[2024-01-25 18:12:12,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg40445026-6ec1-4ac0-a6ff-b440089af753/GCF_003112435.1_ASM311243v1_genomic.fna.gz --refList GCF_003112435.1_ASM311243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003112435.1_ASM311243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:31,958] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:31,975] [INFO] Found 31 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:31,975] [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_003112435.1	s__Novimethylophilus kurashikiensis	100.0	1212	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Novimethylophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001645185.1	s__MM2 sp001645185	78.3271	273	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__MM2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730115.1	s__Pseudomethylobacillus aquaticus	77.6027	158	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168195.1	s__CABHOJ01 sp902168195	77.5579	128	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CABHOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	77.5143	163	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764585.1	s__Sulfurimicrobium lacus	77.2003	147	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704575.1	s__UBA6140 sp001704575	77.1583	156	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	77.0866	105	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCF_009800965.1	s__Azoarcus_E halotolerans	77.0776	69	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_E	95.0	97.94	97.94	0.86	0.86	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	77.0663	103	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617925.1	s__Methylobacillus glycogenes	77.0386	103	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274805.1	s__Oryzomicrobium terrae	76.9956	114	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Oryzomicrobium	95.0	98.48	98.48	0.93	0.93	2	-
GCF_000013705.1	s__Methylobacillus flagellatus	76.9174	127	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCA_903834185.1	s__CAILHX01 sp903834185	76.8584	97	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CAILHX01	95.0	99.93	99.93	0.94	0.94	2	-
GCF_009469585.1	s__Azonexus sp009469585	76.839	126	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938015.1	s__Sulfuriferula plumbiphila	76.7436	99	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971475.1	s__Sulfuricella sp000971475	76.7396	115	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251695.1	s__Ralstonia solanacearum	76.727	106	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.27	95.49	0.87	0.78	131	-
GCA_016234655.1	s__Sulfuritortus sp016234655	76.6893	107	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653115.1	s__Rhodocyclus purpureus	76.689	110	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721185.1	s__Azonexus sp016721185	76.6704	64	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.23	97.74	0.89	0.86	3	-
GCA_017880825.1	s__JADGRN01 sp017880825	76.6466	84	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JADGRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335435.1	s__Parasulfuritortus sp013335435	76.6255	100	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876015.1	s__Cupriavidus basilensis_B	76.4964	143	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCA_016791065.1	s__Azonexus sp016791065	76.4001	87	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746125.1	s__Casimicrobium huifangae	76.3914	63	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__Casimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851125.1	s__Sulfuriferula multivorans	76.3196	84	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377585.1	s__WYBJ01 sp009377585	76.3104	59	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__WYBJ01;g__WYBJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377645.1	s__Thiomonas sp000377645	76.3055	73	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCF_001584185.1	s__Collimonas pratensis	76.218	96	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_015354335.1	s__Methylophilus sp015354335	76.0773	67	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:31,977] [INFO] GTDB search result was written to GCF_003112435.1_ASM311243v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:31,977] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:31,982] [INFO] DFAST_QC result json was written to GCF_003112435.1_ASM311243v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:31,982] [INFO] DFAST_QC completed!
[2024-01-25 18:12:31,983] [INFO] Total running time: 0h1m26s