[2024-01-24 11:20:49,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference
[2024-01-24 11:20:51,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,111] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,112] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f807a75-5efb-4217-b297-881515d1f70f/GCF_002028405.1_ASM202840v1_genomic.fna.gz | prodigal -d GCF_002028405.1_ASM202840v1_genomic.fna/cds.fna -a GCF_002028405.1_ASM202840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:02,113] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:02,113] [INFO] Task started: HMMsearch
[2024-01-24 11:21:02,114] [INFO] Running command: hmmsearch --tblout GCF_002028405.1_ASM202840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/reference_markers.hmm GCF_002028405.1_ASM202840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:02,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:02,384] [INFO] Found 6/6 markers.
[2024-01-24 11:21:02,416] [INFO] Query marker FASTA was written to GCF_002028405.1_ASM202840v1_genomic.fna/markers.fasta
[2024-01-24 11:21:02,416] [INFO] Task started: Blastn
[2024-01-24 11:21:02,416] [INFO] Running command: blastn -query GCF_002028405.1_ASM202840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/reference_markers.fasta -out GCF_002028405.1_ASM202840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:03,322] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:03,326] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:03,326] [INFO] Target genome list was writen to GCF_002028405.1_ASM202840v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:03,334] [INFO] Task started: fastANI
[2024-01-24 11:21:03,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f807a75-5efb-4217-b297-881515d1f70f/GCF_002028405.1_ASM202840v1_genomic.fna.gz --refList GCF_002028405.1_ASM202840v1_genomic.fna/target_genomes.txt --output GCF_002028405.1_ASM202840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:17,405] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:17,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:17,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:17,422] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:17,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:17,422] [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
Thiomonas intermedia	strain=ATCC 15466	GCA_002028405.1	926	926	type	True	100.0	1113	1114	95	conclusive
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001517285.1	339866	339866	type	True	87.665	846	1114	95	below_threshold
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001418255.1	339866	339866	type	True	87.6606	846	1114	95	below_threshold
Thiomonas arsenitoxydans	strain=3As	GCA_000253115.1	426114	426114	type	True	85.5528	824	1114	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.7452	303	1114	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	77.4486	279	1114	95	below_threshold
Comamonas serinivorans	strain=DSM 26136	GCA_002158865.1	1082851	1082851	type	True	77.3947	216	1114	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.3493	290	1114	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	77.2975	268	1114	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.2788	247	1114	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	77.2575	288	1114	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.002	187	1114	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.8721	217	1114	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	76.7837	161	1114	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	76.3446	195	1114	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2818	253	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:17,424] [INFO] DFAST Taxonomy check result was written to GCF_002028405.1_ASM202840v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:17,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:17,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:17,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/checkm_data
[2024-01-24 11:21:17,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:17,465] [INFO] Task started: CheckM
[2024-01-24 11:21:17,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002028405.1_ASM202840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002028405.1_ASM202840v1_genomic.fna/checkm_input GCF_002028405.1_ASM202840v1_genomic.fna/checkm_result
[2024-01-24 11:22:02,531] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:02,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:02,555] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:02,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:02,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002028405.1_ASM202840v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:02,556] [INFO] Task started: Blastn
[2024-01-24 11:22:02,557] [INFO] Running command: blastn -query GCF_002028405.1_ASM202840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76fe94f-79ed-4889-9490-656bfab4abc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002028405.1_ASM202840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:04,253] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:04,257] [INFO] Selected 9 target genomes.
[2024-01-24 11:22:04,258] [INFO] Target genome list was writen to GCF_002028405.1_ASM202840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:04,282] [INFO] Task started: fastANI
[2024-01-24 11:22:04,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f807a75-5efb-4217-b297-881515d1f70f/GCF_002028405.1_ASM202840v1_genomic.fna.gz --refList GCF_002028405.1_ASM202840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002028405.1_ASM202840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:10,700] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:10,714] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:10,714] [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_002028405.1	s__Thiomonas intermedia	100.0	1113	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001418255.1	s__Thiomonas bhubaneswarensis	87.6466	847	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000253115.1	s__Thiomonas arsenitoxydans	85.566	823	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	97.73	96.84	0.88	0.81	19	-
GCA_016936875.1	s__Thiomonas sp016936875	83.9742	616	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334805.1	s__Thiomonas sp011334805	83.9693	410	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089495.1	s__Thiomonas sp900089495	80.0106	511	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261475.1	s__Bordetella sp002261475	76.8165	199	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCA_004298295.1	s__2-02-FULL-66-14 sp004298295	76.1665	71	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-02-FULL-66-14	95.0	96.40	96.40	0.72	0.72	2	-
GCA_004298325.1	s__2-02-FULL-66-14 sp004298325	75.9947	94	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-02-FULL-66-14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:10,716] [INFO] GTDB search result was written to GCF_002028405.1_ASM202840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:10,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:10,720] [INFO] DFAST_QC result json was written to GCF_002028405.1_ASM202840v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:10,720] [INFO] DFAST_QC completed!
[2024-01-24 11:22:10,720] [INFO] Total running time: 0h1m21s