[2024-01-25 18:57:35,911] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:35,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:35,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference
[2024-01-25 18:57:37,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:37,135] [INFO] Task started: Prodigal
[2024-01-25 18:57:37,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgce4e4ef0-0177-4611-9cdd-48f963c6e10c/GCF_020539505.1_ASM2053950v1_genomic.fna.gz | prodigal -d GCF_020539505.1_ASM2053950v1_genomic.fna/cds.fna -a GCF_020539505.1_ASM2053950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:46,121] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:46,122] [INFO] Task started: HMMsearch
[2024-01-25 18:57:46,122] [INFO] Running command: hmmsearch --tblout GCF_020539505.1_ASM2053950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/reference_markers.hmm GCF_020539505.1_ASM2053950v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:46,347] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:46,348] [INFO] Found 6/6 markers.
[2024-01-25 18:57:46,374] [INFO] Query marker FASTA was written to GCF_020539505.1_ASM2053950v1_genomic.fna/markers.fasta
[2024-01-25 18:57:46,375] [INFO] Task started: Blastn
[2024-01-25 18:57:46,375] [INFO] Running command: blastn -query GCF_020539505.1_ASM2053950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/reference_markers.fasta -out GCF_020539505.1_ASM2053950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:47,125] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:47,128] [INFO] Selected 20 target genomes.
[2024-01-25 18:57:47,128] [INFO] Target genome list was writen to GCF_020539505.1_ASM2053950v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:47,143] [INFO] Task started: fastANI
[2024-01-25 18:57:47,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4e4ef0-0177-4611-9cdd-48f963c6e10c/GCF_020539505.1_ASM2053950v1_genomic.fna.gz --refList GCF_020539505.1_ASM2053950v1_genomic.fna/target_genomes.txt --output GCF_020539505.1_ASM2053950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:59,832] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:59,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:59,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:59,844] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:59,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:59,844] [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 faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	100.0	1032	1032	95	conclusive
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	78.4818	296	1032	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	77.9976	195	1032	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	77.9923	271	1032	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	77.9676	195	1032	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	77.9662	269	1032	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	77.9549	265	1032	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.8146	172	1032	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	77.6937	154	1032	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	77.3863	183	1032	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	77.3783	169	1032	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	77.3588	161	1032	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	77.3125	184	1032	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.3008	159	1032	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	77.2865	186	1032	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.2511	160	1032	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	76.9076	64	1032	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	76.4688	77	1032	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	76.0834	65	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:59,845] [INFO] DFAST Taxonomy check result was written to GCF_020539505.1_ASM2053950v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:59,846] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:59,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:59,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/checkm_data
[2024-01-25 18:57:59,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:59,879] [INFO] Task started: CheckM
[2024-01-25 18:57:59,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020539505.1_ASM2053950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020539505.1_ASM2053950v1_genomic.fna/checkm_input GCF_020539505.1_ASM2053950v1_genomic.fna/checkm_result
[2024-01-25 18:58:28,794] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:28,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:28,813] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:28,813] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:28,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020539505.1_ASM2053950v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:28,816] [INFO] Task started: Blastn
[2024-01-25 18:58:28,816] [INFO] Running command: blastn -query GCF_020539505.1_ASM2053950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg143a2d6b-1251-4c0b-b425-65bc5b679dba/dqc_reference/reference_markers_gtdb.fasta -out GCF_020539505.1_ASM2053950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:30,278] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:30,281] [INFO] Selected 27 target genomes.
[2024-01-25 18:58:30,281] [INFO] Target genome list was writen to GCF_020539505.1_ASM2053950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:30,308] [INFO] Task started: fastANI
[2024-01-25 18:58:30,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4e4ef0-0177-4611-9cdd-48f963c6e10c/GCF_020539505.1_ASM2053950v1_genomic.fna.gz --refList GCF_020539505.1_ASM2053950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020539505.1_ASM2053950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:51,504] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:51,520] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:58:51,520] [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_003545815.1	s__Pusillimonas caeni	78.4952	295	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	78.2994	174	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_900078705.1	s__Bordetella_B ansorpii_A	78.2668	199	1032	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_900129885.1	s__Candidimonas_A bauzanensis	78.2042	192	1032	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_017745595.1	s__Bordetella_A petrii_C	78.0432	207	1032	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_003096595.1	s__Pusillimonas noertemannii	77.9923	271	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_013416525.1	s__Parapusillimonas granuli	77.9728	194	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013416455.1	s__JACCES01 sp013416455	77.9145	156	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JACCES01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119665.1	s__Bordetella_B sp002119665	77.8696	192	1032	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_019166065.1	s__Candidimonas humi	77.8146	172	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	77.7659	184	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	77.6614	183	1032	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_001270295.1	s__Achromobacter sp001270295	77.5249	147	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859765.1	s__Achromobacter pulmonis	77.4063	168	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
GCF_002261265.1	s__Bordetella_A sp002261265	77.3914	165	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.22	99.22	0.95	0.94	3	-
GCF_007679965.1	s__Bordetella_B sp007679965	77.3128	182	1032	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_019218885.1	s__Bordetella_A sp019218885	77.3086	179	1032	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_000306945.1	s__Bordetella pertussis	77.2869	158	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_012928505.1	s__Achromobacter sp012928505	77.2831	156	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592225.1	s__Castellaniella caeni	77.2724	159	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.69	99.69	0.95	0.95	2	-
GCF_002261225.1	s__Bordetella_C sp002261225	77.2436	157	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002188635.1	s__Pigmentiphaga sp002188635	77.2141	140	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.65	99.31	0.97	0.93	3	-
GCF_001548475.1	s__Bordetella hinzii	77.2115	173	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_900078335.1	s__Bordetella trematum	77.1962	152	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
GCA_009360345.1	s__Pigmentiphaga sp009360345	77.0181	127	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.85	99.84	0.97	0.96	3	-
GCF_009497775.1	s__Alcaligenes faecalis_D	77.0112	139	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854895.1	s__Pigmentiphaga sp003854895	76.68	132	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:51,521] [INFO] GTDB search result was written to GCF_020539505.1_ASM2053950v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:51,522] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:51,526] [INFO] DFAST_QC result json was written to GCF_020539505.1_ASM2053950v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:51,526] [INFO] DFAST_QC completed!
[2024-01-25 18:58:51,526] [INFO] Total running time: 0h1m16s