[2024-01-24 10:47:24,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference
[2024-01-24 10:47:26,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,259] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,260] [INFO] Running command: gunzip -c /var/lib/cwl/stgc57fdb6d-a824-459a-8b9c-583ed3450b43/GCF_019166065.1_ASM1916606v1_genomic.fna.gz | prodigal -d GCF_019166065.1_ASM1916606v1_genomic.fna/cds.fna -a GCF_019166065.1_ASM1916606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:41,491] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:41,491] [INFO] Task started: HMMsearch
[2024-01-24 10:47:41,491] [INFO] Running command: hmmsearch --tblout GCF_019166065.1_ASM1916606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/reference_markers.hmm GCF_019166065.1_ASM1916606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:41,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:41,808] [INFO] Found 6/6 markers.
[2024-01-24 10:47:41,848] [INFO] Query marker FASTA was written to GCF_019166065.1_ASM1916606v1_genomic.fna/markers.fasta
[2024-01-24 10:47:41,849] [INFO] Task started: Blastn
[2024-01-24 10:47:41,849] [INFO] Running command: blastn -query GCF_019166065.1_ASM1916606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/reference_markers.fasta -out GCF_019166065.1_ASM1916606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:42,826] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:42,830] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:42,830] [INFO] Target genome list was writen to GCF_019166065.1_ASM1916606v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,889] [INFO] Task started: fastANI
[2024-01-24 10:47:42,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgc57fdb6d-a824-459a-8b9c-583ed3450b43/GCF_019166065.1_ASM1916606v1_genomic.fna.gz --refList GCF_019166065.1_ASM1916606v1_genomic.fna/target_genomes.txt --output GCF_019166065.1_ASM1916606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:01,771] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:01,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:01,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:01,797] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:01,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:01,798] [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
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	100.0	1554	1556	95	conclusive
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	87.5868	1122	1556	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.8176	526	1556	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.7624	617	1556	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.7467	524	1556	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	79.6676	463	1556	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.5663	515	1556	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	79.3993	560	1556	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	79.2367	566	1556	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	79.2157	579	1556	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	79.0427	527	1556	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.9686	517	1556	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.3917	400	1556	95	below_threshold
Bordetella avium	strain=NCTC12033	GCA_900445835.1	521	521	type	True	78.1331	291	1556	95	below_threshold
Bordetella avium	strain=HAMBI_2160	GCA_003350095.1	521	521	type	True	78.1084	292	1556	95	below_threshold
Bordetella avium	strain=ATCC 35086	GCA_003581385.1	521	521	type	True	78.071	296	1556	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.9715	213	1556	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	76.6778	139	1556	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.0517	131	1556	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.6774	152	1556	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	75.4074	87	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:01,800] [INFO] DFAST Taxonomy check result was written to GCF_019166065.1_ASM1916606v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:01,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:01,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:01,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/checkm_data
[2024-01-24 10:48:01,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:01,856] [INFO] Task started: CheckM
[2024-01-24 10:48:01,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019166065.1_ASM1916606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019166065.1_ASM1916606v1_genomic.fna/checkm_input GCF_019166065.1_ASM1916606v1_genomic.fna/checkm_result
[2024-01-24 10:48:45,297] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:45,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,324] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:45,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:45,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019166065.1_ASM1916606v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:45,325] [INFO] Task started: Blastn
[2024-01-24 10:48:45,326] [INFO] Running command: blastn -query GCF_019166065.1_ASM1916606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2573765e-bce7-467a-8f28-246d06987d81/dqc_reference/reference_markers_gtdb.fasta -out GCF_019166065.1_ASM1916606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,996] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:47,001] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:47,001] [INFO] Target genome list was writen to GCF_019166065.1_ASM1916606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:47,029] [INFO] Task started: fastANI
[2024-01-24 10:48:47,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgc57fdb6d-a824-459a-8b9c-583ed3450b43/GCF_019166065.1_ASM1916606v1_genomic.fna.gz --refList GCF_019166065.1_ASM1916606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019166065.1_ASM1916606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:04,038] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:04,059] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:04,060] [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_019166065.1	s__Candidimonas humi	100.0	1554	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002209565.1	s__Candidimonas nitroreducens	87.5865	1122	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203015.1	s__Castellaniella defragrans	79.9067	496	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_013416525.1	s__Parapusillimonas granuli	79.7662	522	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001270295.1	s__Achromobacter sp001270295	79.7533	459	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745595.1	s__Bordetella_A petrii_C	79.7495	545	1556	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_002261345.1	s__Bordetella_A sp002261345	79.7345	598	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_003545815.1	s__Pusillimonas caeni	79.73	458	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.591	602	1556	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	79.5001	452	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	99.25	97.76	0.97	0.91	4	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.3453	534	1556	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_002261225.1	s__Bordetella_C sp002261225	79.162	576	1556	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_001548475.1	s__Bordetella hinzii	79.0706	508	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCA_013416455.1	s__JACCES01 sp013416455	79.0485	412	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JACCES01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236785.1	s__Achromobacter arsenitoxydans	78.9809	523	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376425.1	s__Thiobacillus denitrificans	76.6613	141	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001530125.1	s__Thiobacillus denitrificans_C	76.3991	142	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820745.1	s__Thiobacillus sp018820745	75.8998	62	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:04,061] [INFO] GTDB search result was written to GCF_019166065.1_ASM1916606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:04,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:04,066] [INFO] DFAST_QC result json was written to GCF_019166065.1_ASM1916606v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:04,066] [INFO] DFAST_QC completed!
[2024-01-24 10:49:04,066] [INFO] Total running time: 0h1m40s