[2024-01-24 14:10:15,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference
[2024-01-24 14:10:16,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:16,740] [INFO] Task started: Prodigal
[2024-01-24 14:10:16,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg1810985a-5bad-4541-95bd-201579c8f5b4/GCF_021653995.1_ASM2165399v1_genomic.fna.gz | prodigal -d GCF_021653995.1_ASM2165399v1_genomic.fna/cds.fna -a GCF_021653995.1_ASM2165399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:31,015] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:31,015] [INFO] Task started: HMMsearch
[2024-01-24 14:10:31,015] [INFO] Running command: hmmsearch --tblout GCF_021653995.1_ASM2165399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/reference_markers.hmm GCF_021653995.1_ASM2165399v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:31,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:31,293] [INFO] Found 6/6 markers.
[2024-01-24 14:10:31,333] [INFO] Query marker FASTA was written to GCF_021653995.1_ASM2165399v1_genomic.fna/markers.fasta
[2024-01-24 14:10:31,334] [INFO] Task started: Blastn
[2024-01-24 14:10:31,334] [INFO] Running command: blastn -query GCF_021653995.1_ASM2165399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/reference_markers.fasta -out GCF_021653995.1_ASM2165399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:32,275] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:32,278] [INFO] Selected 26 target genomes.
[2024-01-24 14:10:32,279] [INFO] Target genome list was writen to GCF_021653995.1_ASM2165399v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:32,308] [INFO] Task started: fastANI
[2024-01-24 14:10:32,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg1810985a-5bad-4541-95bd-201579c8f5b4/GCF_021653995.1_ASM2165399v1_genomic.fna.gz --refList GCF_021653995.1_ASM2165399v1_genomic.fna/target_genomes.txt --output GCF_021653995.1_ASM2165399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:52,237] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:52,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:52,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:52,257] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:10:52,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:10:52,257] [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
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.1635	459	1366	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.1208	450	1366	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	78.9488	329	1366	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	78.8354	412	1366	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	78.6623	354	1366	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	78.579	324	1366	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	78.4425	337	1366	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.3934	386	1366	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	78.3807	318	1366	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.3568	410	1366	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	78.2117	345	1366	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.2058	346	1366	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	78.0903	340	1366	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	78.0592	332	1366	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	77.9222	379	1366	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.9078	161	1366	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.8999	388	1366	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	77.8882	388	1366	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	77.8878	361	1366	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	77.7957	301	1366	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	77.7379	388	1366	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900078335.1	123899	123899	type	True	77.5888	295	1366	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	77.3331	254	1366	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	77.1267	217	1366	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.7899	176	1366	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.7359	172	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:52,259] [INFO] DFAST Taxonomy check result was written to GCF_021653995.1_ASM2165399v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:52,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:52,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:52,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/checkm_data
[2024-01-24 14:10:52,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:52,308] [INFO] Task started: CheckM
[2024-01-24 14:10:52,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021653995.1_ASM2165399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021653995.1_ASM2165399v1_genomic.fna/checkm_input GCF_021653995.1_ASM2165399v1_genomic.fna/checkm_result
[2024-01-24 14:11:34,301] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:34,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:34,320] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:34,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:34,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021653995.1_ASM2165399v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:34,322] [INFO] Task started: Blastn
[2024-01-24 14:11:34,322] [INFO] Running command: blastn -query GCF_021653995.1_ASM2165399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg700b65c4-6a81-4f0d-9f59-55a7b247a83a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021653995.1_ASM2165399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:36,079] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:36,088] [INFO] Selected 19 target genomes.
[2024-01-24 14:11:36,088] [INFO] Target genome list was writen to GCF_021653995.1_ASM2165399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:36,151] [INFO] Task started: fastANI
[2024-01-24 14:11:36,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg1810985a-5bad-4541-95bd-201579c8f5b4/GCF_021653995.1_ASM2165399v1_genomic.fna.gz --refList GCF_021653995.1_ASM2165399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021653995.1_ASM2165399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:51,731] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:51,750] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:51,750] [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_009857885.1	s__Pusillimonas_B sp009857885	99.8365	1276	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013416435.1	s__Parapusillimonas sp013416435	79.2844	382	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	79.1208	450	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003096595.1	s__Pusillimonas noertemannii	78.9371	334	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	78.8455	411	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545815.1	s__Pusillimonas caeni	78.6695	354	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067205.1	s__Bordetella_A petrii	78.5412	371	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	78.3831	387	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342005.1	s__Paracandidimonas soli	78.3807	318	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paracandidimonas	95.0	98.75	98.75	0.86	0.86	2	-
GCF_002209565.1	s__Candidimonas nitroreducens	78.3659	409	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153445.1	s__Pusillimonas_B soli	78.2837	380	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002119665.1	s__Bordetella_B sp002119665	78.2338	336	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261475.1	s__Bordetella sp002261475	78.1143	310	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_001548475.1	s__Bordetella hinzii	78.0592	332	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_902859645.1	s__Achromobacter insuavis	77.9224	380	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_902859765.1	s__Achromobacter pulmonis	77.8971	360	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
GCA_002441445.1	s__UBA6240 sp002441445	77.6702	295	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA6240	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119725.1	s__Bordetella_C sp002119725	77.6613	260	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	98.76	98.76	0.96	0.96	2	-
GCF_900078335.1	s__Bordetella trematum	77.5879	295	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:51,752] [INFO] GTDB search result was written to GCF_021653995.1_ASM2165399v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:51,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:51,764] [INFO] DFAST_QC result json was written to GCF_021653995.1_ASM2165399v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:51,764] [INFO] DFAST_QC completed!
[2024-01-24 14:11:51,765] [INFO] Total running time: 0h1m36s