[2024-01-24 14:06:04,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:04,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:04,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference
[2024-01-24 14:06:05,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:05,685] [INFO] Task started: Prodigal
[2024-01-24 14:06:05,686] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf4ca3ef-e295-463e-b10e-8d8fd0066707/GCF_014237865.1_ASM1423786v1_genomic.fna.gz | prodigal -d GCF_014237865.1_ASM1423786v1_genomic.fna/cds.fna -a GCF_014237865.1_ASM1423786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,484] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,485] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,485] [INFO] Running command: hmmsearch --tblout GCF_014237865.1_ASM1423786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/reference_markers.hmm GCF_014237865.1_ASM1423786v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,833] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,869] [INFO] Query marker FASTA was written to GCF_014237865.1_ASM1423786v1_genomic.fna/markers.fasta
[2024-01-24 14:06:16,869] [INFO] Task started: Blastn
[2024-01-24 14:06:16,870] [INFO] Running command: blastn -query GCF_014237865.1_ASM1423786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/reference_markers.fasta -out GCF_014237865.1_ASM1423786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,686] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,690] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:17,691] [INFO] Target genome list was writen to GCF_014237865.1_ASM1423786v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,703] [INFO] Task started: fastANI
[2024-01-24 14:06:17,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf4ca3ef-e295-463e-b10e-8d8fd0066707/GCF_014237865.1_ASM1423786v1_genomic.fna.gz --refList GCF_014237865.1_ASM1423786v1_genomic.fna/target_genomes.txt --output GCF_014237865.1_ASM1423786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,172] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,188] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:36,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:36,188] [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 minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	100.0	1042	1044	95	conclusive
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.597	309	1044	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.5141	232	1044	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.4125	230	1044	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	78.383	288	1044	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	78.1191	183	1044	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	78.0526	290	1044	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	78.0495	293	1044	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	78.0103	200	1044	95	below_threshold
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	77.9666	236	1044	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.8118	218	1044	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.499	248	1044	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	77.2609	54	1044	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	76.4555	69	1044	95	below_threshold
Paraburkholderia antibiotica	strain=G-4-1-8	GCA_012927125.1	2728839	2728839	type	True	76.2849	53	1044	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.1513	65	1044	95	below_threshold
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	75.8642	59	1044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,191] [INFO] DFAST Taxonomy check result was written to GCF_014237865.1_ASM1423786v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/checkm_data
[2024-01-24 14:06:36,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:36,228] [INFO] Task started: CheckM
[2024-01-24 14:06:36,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014237865.1_ASM1423786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014237865.1_ASM1423786v1_genomic.fna/checkm_input GCF_014237865.1_ASM1423786v1_genomic.fna/checkm_result
[2024-01-24 14:07:10,430] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:10,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:10,451] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:10,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:10,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014237865.1_ASM1423786v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:10,452] [INFO] Task started: Blastn
[2024-01-24 14:07:10,453] [INFO] Running command: blastn -query GCF_014237865.1_ASM1423786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2241398-98ee-4ab8-8c8a-90bf963fc3df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014237865.1_ASM1423786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:11,765] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:11,768] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:11,769] [INFO] Target genome list was writen to GCF_014237865.1_ASM1423786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:11,787] [INFO] Task started: fastANI
[2024-01-24 14:07:11,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf4ca3ef-e295-463e-b10e-8d8fd0066707/GCF_014237865.1_ASM1423786v1_genomic.fna.gz --refList GCF_014237865.1_ASM1423786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014237865.1_ASM1423786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:25,742] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:25,760] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:25,760] [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_014237865.1	s__Pusillimonas_A sp014237865	100.0	1043	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002236805.1	s__Pusillimonas_A sp002236805	89.4515	812	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCA_012744285.1	s__Pusillimonas_A sp012744285	79.6556	356	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315175.1	s__Eoetvoesia caeni	78.5284	304	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013416525.1	s__Parapusillimonas granuli	78.3954	231	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	78.3498	215	1044	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_003545815.1	s__Pusillimonas caeni	78.3433	291	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416405.1	s__Pusillimonas_C sp013416405	78.1261	213	1044	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_003576595.1	s__Pusillimonas_A maritima	77.9666	236	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	-
GCA_013416435.1	s__Parapusillimonas sp013416435	77.9087	214	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	77.7813	220	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727555.1	s__JAAYGT01 sp012727555	77.7025	192	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAYGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261355.1	s__Bordetella sp002261355	77.6962	160	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209565.1	s__Candidimonas nitroreducens	77.5023	247	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119665.1	s__Bordetella_B sp002119665	77.4038	193	1044	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_017745595.1	s__Bordetella_A petrii_C	77.3775	243	1044	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_002975275.1	s__Achromobacter sp002975275	77.3198	171	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:25,762] [INFO] GTDB search result was written to GCF_014237865.1_ASM1423786v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:25,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:25,767] [INFO] DFAST_QC result json was written to GCF_014237865.1_ASM1423786v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:25,768] [INFO] DFAST_QC completed!
[2024-01-24 14:07:25,768] [INFO] Total running time: 0h1m21s