[2024-01-24 14:19:02,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference
[2024-01-24 14:19:03,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,689] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,689] [INFO] Running command: gunzip -c /var/lib/cwl/stgc28d429f-6294-4884-92b5-5372eab7ad75/GCF_004153455.1_ASM415345v1_genomic.fna.gz | prodigal -d GCF_004153455.1_ASM415345v1_genomic.fna/cds.fna -a GCF_004153455.1_ASM415345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:18,647] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:18,647] [INFO] Task started: HMMsearch
[2024-01-24 14:19:18,647] [INFO] Running command: hmmsearch --tblout GCF_004153455.1_ASM415345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/reference_markers.hmm GCF_004153455.1_ASM415345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:18,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:18,991] [INFO] Found 6/6 markers.
[2024-01-24 14:19:19,032] [INFO] Query marker FASTA was written to GCF_004153455.1_ASM415345v1_genomic.fna/markers.fasta
[2024-01-24 14:19:19,033] [INFO] Task started: Blastn
[2024-01-24 14:19:19,033] [INFO] Running command: blastn -query GCF_004153455.1_ASM415345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/reference_markers.fasta -out GCF_004153455.1_ASM415345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:19,911] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:19,914] [INFO] Selected 22 target genomes.
[2024-01-24 14:19:19,915] [INFO] Target genome list was writen to GCF_004153455.1_ASM415345v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:19,923] [INFO] Task started: fastANI
[2024-01-24 14:19:19,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28d429f-6294-4884-92b5-5372eab7ad75/GCF_004153455.1_ASM415345v1_genomic.fna.gz --refList GCF_004153455.1_ASM415345v1_genomic.fna/target_genomes.txt --output GCF_004153455.1_ASM415345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:36,786] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:36,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:36,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:36,803] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:36,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:36,804] [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 ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	100.0	1488	1491	95	conclusive
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	79.9218	294	1491	95	below_threshold
Pusillimonas soli	strain=DSM 25264	GCA_013416335.1	659016	659016	type	True	79.1145	420	1491	95	below_threshold
Pusillimonas soli	strain=KCTC 22455	GCA_004153445.1	659016	659016	type	True	79.1097	423	1491	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.9548	386	1491	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.8434	388	1491	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	78.3878	260	1491	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	78.3831	254	1491	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_013416295.1	305977	305977	type	True	78.3695	258	1491	95	below_threshold
Kerstersia gyiorum	strain=DSM 16618	GCA_004216755.1	206506	206506	type	True	78.3034	171	1491	95	below_threshold
Kerstersia gyiorum	strain=CCUG 47000	GCA_008801725.1	206506	206506	type	True	78.2757	175	1491	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.1073	167	1491	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.0716	336	1491	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.9562	336	1491	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	77.8524	273	1491	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	77.6406	300	1491	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.6073	246	1491	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	77.5586	266	1491	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.3364	68	1491	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	76.2099	79	1491	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	75.942	81	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:36,806] [INFO] DFAST Taxonomy check result was written to GCF_004153455.1_ASM415345v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:36,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:36,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:36,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/checkm_data
[2024-01-24 14:19:36,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:36,868] [INFO] Task started: CheckM
[2024-01-24 14:19:36,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004153455.1_ASM415345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004153455.1_ASM415345v1_genomic.fna/checkm_input GCF_004153455.1_ASM415345v1_genomic.fna/checkm_result
[2024-01-24 14:20:25,572] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:25,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:25,598] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:25,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:25,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004153455.1_ASM415345v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:25,599] [INFO] Task started: Blastn
[2024-01-24 14:20:25,599] [INFO] Running command: blastn -query GCF_004153455.1_ASM415345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg137e0fcf-61d7-426c-af81-0533e422af7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004153455.1_ASM415345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:27,246] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:27,250] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:27,250] [INFO] Target genome list was writen to GCF_004153455.1_ASM415345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:27,265] [INFO] Task started: fastANI
[2024-01-24 14:20:27,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28d429f-6294-4884-92b5-5372eab7ad75/GCF_004153455.1_ASM415345v1_genomic.fna.gz --refList GCF_004153455.1_ASM415345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004153455.1_ASM415345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:41,143] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:41,157] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:41,158] [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_004153455.1	s__Pusillimonas_B ginsengisoli	100.0	1488	1491	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
GCF_003545815.1	s__Pusillimonas caeni	79.9218	294	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	79.7525	331	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_004153445.1	s__Pusillimonas_B soli	79.0984	424	1491	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_009857885.1	s__Pusillimonas_B sp009857885	78.858	407	1491	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	78.8434	388	1491	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	78.655	370	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096595.1	s__Pusillimonas noertemannii	78.3878	260	1491	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	78.3643	398	1491	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_004216755.1	s__Kerstersia gyiorum	78.328	171	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kerstersia	95.0	98.96	97.89	0.94	0.91	5	-
GCA_013416445.1	s__Candidimonas_A sp013416445	78.157	266	1491	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	78.0672	337	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	78.0083	309	1491	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_019166065.1	s__Candidimonas humi	77.967	335	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859695.1	s__Achromobacter ruhlandii	77.844	275	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_000306945.1	s__Bordetella pertussis	77.6107	245	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCA_002441445.1	s__UBA6240 sp002441445	77.3322	271	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA6240	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,159] [INFO] GTDB search result was written to GCF_004153455.1_ASM415345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:41,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:41,167] [INFO] DFAST_QC result json was written to GCF_004153455.1_ASM415345v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:41,168] [INFO] DFAST_QC completed!
[2024-01-24 14:20:41,168] [INFO] Total running time: 0h1m39s