[2024-01-24 14:22:32,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:32,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:32,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference
[2024-01-24 14:22:33,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:33,995] [INFO] Task started: Prodigal
[2024-01-24 14:22:33,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg40acf1d4-5e45-420c-8582-8cf2559f304d/GCF_004022565.1_ASM402256v1_genomic.fna.gz | prodigal -d GCF_004022565.1_ASM402256v1_genomic.fna/cds.fna -a GCF_004022565.1_ASM402256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,980] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,980] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,980] [INFO] Running command: hmmsearch --tblout GCF_004022565.1_ASM402256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/reference_markers.hmm GCF_004022565.1_ASM402256v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:46,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:46,295] [INFO] Found 6/6 markers.
[2024-01-24 14:22:46,337] [INFO] Query marker FASTA was written to GCF_004022565.1_ASM402256v1_genomic.fna/markers.fasta
[2024-01-24 14:22:46,337] [INFO] Task started: Blastn
[2024-01-24 14:22:46,338] [INFO] Running command: blastn -query GCF_004022565.1_ASM402256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/reference_markers.fasta -out GCF_004022565.1_ASM402256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:47,555] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:47,562] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:47,562] [INFO] Target genome list was writen to GCF_004022565.1_ASM402256v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:47,571] [INFO] Task started: fastANI
[2024-01-24 14:22:47,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg40acf1d4-5e45-420c-8582-8cf2559f304d/GCF_004022565.1_ASM402256v1_genomic.fna.gz --refList GCF_004022565.1_ASM402256v1_genomic.fna/target_genomes.txt --output GCF_004022565.1_ASM402256v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:02,550] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:02,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:02,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:02,568] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:02,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:02,568] [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
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	79.929	352	1182	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	79.6797	201	1182	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	79.5783	337	1182	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.4912	477	1182	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.3986	484	1182	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.9912	324	1182	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	78.9528	328	1182	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	78.9407	327	1182	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	78.6984	343	1182	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	78.5972	344	1182	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.2319	363	1182	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.0779	338	1182	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	77.8465	308	1182	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	77.6923	323	1182	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.5697	298	1182	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	77.5127	307	1182	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	77.4964	288	1182	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	76.6853	133	1182	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.5451	126	1182	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	76.3333	120	1182	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	76.3199	95	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:02,570] [INFO] DFAST Taxonomy check result was written to GCF_004022565.1_ASM402256v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:02,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:02,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:02,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/checkm_data
[2024-01-24 14:23:02,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:02,611] [INFO] Task started: CheckM
[2024-01-24 14:23:02,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004022565.1_ASM402256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004022565.1_ASM402256v1_genomic.fna/checkm_input GCF_004022565.1_ASM402256v1_genomic.fna/checkm_result
[2024-01-24 14:23:40,124] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:40,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:40,148] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:40,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:40,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004022565.1_ASM402256v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:40,150] [INFO] Task started: Blastn
[2024-01-24 14:23:40,150] [INFO] Running command: blastn -query GCF_004022565.1_ASM402256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f477b99-6f9b-4fa1-a560-b6e87c7b3361/dqc_reference/reference_markers_gtdb.fasta -out GCF_004022565.1_ASM402256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:41,769] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:41,772] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:41,773] [INFO] Target genome list was writen to GCF_004022565.1_ASM402256v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:41,806] [INFO] Task started: fastANI
[2024-01-24 14:23:41,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg40acf1d4-5e45-420c-8582-8cf2559f304d/GCF_004022565.1_ASM402256v1_genomic.fna.gz --refList GCF_004022565.1_ASM402256v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004022565.1_ASM402256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:55,049] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:55,072] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:55,073] [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_004022565.1	s__Pusillimonas_D thiosulfatoxidans	100.0	1182	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	conclusive
GCF_003545815.1	s__Pusillimonas caeni	79.9594	350	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	79.5929	336	1182	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_013416525.1	s__Parapusillimonas granuli	79.3986	484	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013416435.1	s__Parapusillimonas sp013416435	79.1772	389	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	79.1552	431	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.1031	454	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315175.1	s__Eoetvoesia caeni	78.959	327	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013416445.1	s__Candidimonas_A sp013416445	78.7815	331	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	78.4534	373	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209565.1	s__Candidimonas nitroreducens	78.2112	365	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067205.1	s__Bordetella_A petrii	78.1586	300	1182	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	78.0779	338	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441445.1	s__UBA6240 sp002441445	78.0172	312	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA6240	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	77.8935	298	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:55,086] [INFO] GTDB search result was written to GCF_004022565.1_ASM402256v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:55,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:55,093] [INFO] DFAST_QC result json was written to GCF_004022565.1_ASM402256v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:55,093] [INFO] DFAST_QC completed!
[2024-01-24 14:23:55,093] [INFO] Total running time: 0h1m22s