[2023-06-05 18:35:07,270] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:35:07,276] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:35:07,276] [INFO] DQC Reference Directory: /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference
[2023-06-05 18:35:09,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:35:09,047] [INFO] Task started: Prodigal
[2023-06-05 18:35:09,048] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0c8855e-f43f-4899-babe-6233c59fc802/GCA_004321985.1_ASM432198v1_genomic.fna.gz | prodigal -d GCA_004321985.1_ASM432198v1_genomic.fna/cds.fna -a GCA_004321985.1_ASM432198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:35:19,530] [INFO] Task succeeded: Prodigal
[2023-06-05 18:35:19,530] [INFO] Task started: HMMsearch
[2023-06-05 18:35:19,530] [INFO] Running command: hmmsearch --tblout GCA_004321985.1_ASM432198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/reference_markers.hmm GCA_004321985.1_ASM432198v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:35:19,762] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:35:19,763] [INFO] Found 6/6 markers.
[2023-06-05 18:35:19,792] [INFO] Query marker FASTA was written to GCA_004321985.1_ASM432198v1_genomic.fna/markers.fasta
[2023-06-05 18:35:19,793] [INFO] Task started: Blastn
[2023-06-05 18:35:19,793] [INFO] Running command: blastn -query GCA_004321985.1_ASM432198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/reference_markers.fasta -out GCA_004321985.1_ASM432198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:20,732] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:20,736] [INFO] Selected 23 target genomes.
[2023-06-05 18:35:20,736] [INFO] Target genome list was writen to GCA_004321985.1_ASM432198v1_genomic.fna/target_genomes.txt
[2023-06-05 18:35:20,745] [INFO] Task started: fastANI
[2023-06-05 18:35:20,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c8855e-f43f-4899-babe-6233c59fc802/GCA_004321985.1_ASM432198v1_genomic.fna.gz --refList GCA_004321985.1_ASM432198v1_genomic.fna/target_genomes.txt --output GCA_004321985.1_ASM432198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:35:40,229] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:40,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:35:40,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:35:40,248] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:35:40,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:35:40,248] [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
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	80.5639	489	1096	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	80.5069	517	1096	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	77.8734	260	1096	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	77.853	263	1096	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.8131	302	1096	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.7044	252	1096	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	77.6283	228	1096	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	77.5714	268	1096	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	77.53	295	1096	95	below_threshold
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	77.4665	257	1096	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	77.386	278	1096	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	77.385	254	1096	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	77.3617	229	1096	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	77.3145	285	1096	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	77.2141	294	1096	95	below_threshold
Paralcaligenes ureilyticus	strain=DSM 24591	GCA_004346225.1	627131	627131	type	True	76.3514	161	1096	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	76.3068	133	1096	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	76.1392	135	1096	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.1002	157	1096	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	76.0745	139	1096	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	75.894	133	1096	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	75.7432	124	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:35:40,250] [INFO] DFAST Taxonomy check result was written to GCA_004321985.1_ASM432198v1_genomic.fna/tc_result.tsv
[2023-06-05 18:35:40,253] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:35:40,253] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:35:40,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/checkm_data
[2023-06-05 18:35:40,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:35:40,292] [INFO] Task started: CheckM
[2023-06-05 18:35:40,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004321985.1_ASM432198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004321985.1_ASM432198v1_genomic.fna/checkm_input GCA_004321985.1_ASM432198v1_genomic.fna/checkm_result
[2023-06-05 18:36:16,628] [INFO] Task succeeded: CheckM
[2023-06-05 18:36:16,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:36:16,722] [INFO] ===== Completeness check finished =====
[2023-06-05 18:36:16,722] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:36:16,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004321985.1_ASM432198v1_genomic.fna/markers.fasta)
[2023-06-05 18:36:16,723] [INFO] Task started: Blastn
[2023-06-05 18:36:16,723] [INFO] Running command: blastn -query GCA_004321985.1_ASM432198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc35ee93d-4cd2-48d9-b487-008ce7f4edcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_004321985.1_ASM432198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:36:18,544] [INFO] Task succeeded: Blastn
[2023-06-05 18:36:18,549] [INFO] Selected 17 target genomes.
[2023-06-05 18:36:18,549] [INFO] Target genome list was writen to GCA_004321985.1_ASM432198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:36:18,701] [INFO] Task started: fastANI
[2023-06-05 18:36:18,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c8855e-f43f-4899-babe-6233c59fc802/GCA_004321985.1_ASM432198v1_genomic.fna.gz --refList GCA_004321985.1_ASM432198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004321985.1_ASM432198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:36:40,151] [INFO] Task succeeded: fastANI
[2023-06-05 18:36:40,165] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:36:40,166] [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
GCA_004321985.1	s__Castellaniella sp004321985	100.0	1090	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014203015.1	s__Castellaniella defragrans	80.495	518	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCA_019104865.1	s__Castellaniella sp019104865	79.5269	454	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421865.1	s__Castellaniella sp002421865	79.4425	368	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592225.1	s__Castellaniella caeni	79.366	451	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.69	99.69	0.95	0.95	2	-
GCF_001270295.1	s__Achromobacter sp001270295	77.9763	236	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	77.8172	266	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002209565.1	s__Candidimonas nitroreducens	77.8021	303	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	77.6911	253	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002885955.2	s__Achromobacter pulmonis_A	77.6442	294	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_902859585.1	s__Achromobacter animicus	77.4773	256	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.58	96.10	0.93	0.89	8	-
GCF_900089455.2	s__Orrella dioscoreae	77.4542	248	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Orrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342005.1	s__Paracandidimonas soli	77.3617	229	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paracandidimonas	95.0	98.75	98.75	0.86	0.86	2	-
GCF_001571365.1	s__Achromobacter denitrificans	77.3239	284	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_900496975.1	s__Achromobacter veterisilvae	77.2226	293	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001433395.1	s__Bordetella_C sp001433395	77.0922	224	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002894305.1	s__Comamonas_C sp002894305	76.8633	132	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:36:40,168] [INFO] GTDB search result was written to GCA_004321985.1_ASM432198v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:36:40,168] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:36:40,179] [INFO] DFAST_QC result json was written to GCA_004321985.1_ASM432198v1_genomic.fna/dqc_result.json
[2023-06-05 18:36:40,180] [INFO] DFAST_QC completed!
[2023-06-05 18:36:40,180] [INFO] Total running time: 0h1m33s