[2024-01-25 17:48:21,051] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:21,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:21,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference
[2024-01-25 17:48:22,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:22,241] [INFO] Task started: Prodigal
[2024-01-25 17:48:22,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg63c7ccb1-72c7-4d96-9a73-237d904a35bb/GCF_003123725.1_ASM312372v1_genomic.fna.gz | prodigal -d GCF_003123725.1_ASM312372v1_genomic.fna/cds.fna -a GCF_003123725.1_ASM312372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:32,689] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:32,689] [INFO] Task started: HMMsearch
[2024-01-25 17:48:32,689] [INFO] Running command: hmmsearch --tblout GCF_003123725.1_ASM312372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/reference_markers.hmm GCF_003123725.1_ASM312372v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:32,925] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:32,926] [INFO] Found 6/6 markers.
[2024-01-25 17:48:32,964] [INFO] Query marker FASTA was written to GCF_003123725.1_ASM312372v1_genomic.fna/markers.fasta
[2024-01-25 17:48:32,965] [INFO] Task started: Blastn
[2024-01-25 17:48:32,965] [INFO] Running command: blastn -query GCF_003123725.1_ASM312372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/reference_markers.fasta -out GCF_003123725.1_ASM312372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:33,880] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:33,887] [INFO] Selected 25 target genomes.
[2024-01-25 17:48:33,887] [INFO] Target genome list was writen to GCF_003123725.1_ASM312372v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:33,922] [INFO] Task started: fastANI
[2024-01-25 17:48:33,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c7ccb1-72c7-4d96-9a73-237d904a35bb/GCF_003123725.1_ASM312372v1_genomic.fna.gz --refList GCF_003123725.1_ASM312372v1_genomic.fna/target_genomes.txt --output GCF_003123725.1_ASM312372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:54,983] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:54,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:54,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:55,000] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:55,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:55,000] [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
Corticimicrobacter populi	strain=3d-2-2	GCA_003123725.1	2175229	2175229	type	True	100.0	1175	1176	95	conclusive
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	78.7768	293	1176	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	78.6173	316	1176	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	78.6046	313	1176	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	78.5936	302	1176	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	78.5074	320	1176	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	78.4587	307	1176	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	78.4431	367	1176	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.4327	366	1176	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	78.4247	370	1176	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	78.4236	362	1176	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	78.3955	287	1176	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	78.3759	365	1176	95	below_threshold
Kerstersia gyiorum	strain=DSM 16618	GCA_004216755.1	206506	206506	type	True	78.3512	278	1176	95	below_threshold
Kerstersia gyiorum	strain=CCUG 47000	GCA_008801725.1	206506	206506	type	True	78.3431	272	1176	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.1484	223	1176	95	below_threshold
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	77.9641	314	1176	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.8737	239	1176	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	77.7329	219	1176	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	76.9585	131	1176	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.9353	107	1176	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.8	126	1176	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	76.4435	122	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:55,002] [INFO] DFAST Taxonomy check result was written to GCF_003123725.1_ASM312372v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:55,002] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:55,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:55,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/checkm_data
[2024-01-25 17:48:55,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:55,039] [INFO] Task started: CheckM
[2024-01-25 17:48:55,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003123725.1_ASM312372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003123725.1_ASM312372v1_genomic.fna/checkm_input GCF_003123725.1_ASM312372v1_genomic.fna/checkm_result
[2024-01-25 17:49:32,993] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:32,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:33,014] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:33,015] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:33,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003123725.1_ASM312372v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:33,015] [INFO] Task started: Blastn
[2024-01-25 17:49:33,015] [INFO] Running command: blastn -query GCF_003123725.1_ASM312372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0277a587-8828-43a4-bf69-5e49674ba20a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003123725.1_ASM312372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:34,799] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:34,802] [INFO] Selected 23 target genomes.
[2024-01-25 17:49:34,802] [INFO] Target genome list was writen to GCF_003123725.1_ASM312372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:34,824] [INFO] Task started: fastANI
[2024-01-25 17:49:34,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c7ccb1-72c7-4d96-9a73-237d904a35bb/GCF_003123725.1_ASM312372v1_genomic.fna.gz --refList GCF_003123725.1_ASM312372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003123725.1_ASM312372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:55,691] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:55,711] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:55,711] [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_003123725.1	s__Corticimicrobacter populi	100.0	1175	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Corticimicrobacter	95.0	96.49	96.49	0.90	0.90	2	conclusive
GCF_000306945.1	s__Bordetella pertussis	78.7425	295	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002902905.1	s__Achromobacter sp002902905	78.6647	355	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_002261345.1	s__Bordetella_A sp002261345	78.5308	331	1176	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_000657795.2	s__Bordetella pseudohinzii	78.4584	306	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_001457475.1	s__Achromobacter xylosoxidans	78.4236	362	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_002885955.2	s__Achromobacter pulmonis_A	78.3874	341	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_004121055.1	s__Bordetella_C aloeverae	78.3828	289	1176	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_002261265.1	s__Bordetella_A sp002261265	78.3714	253	1176	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_900156745.1	s__Achromobacter sp900156745	78.3508	322	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.81	97.81	0.91	0.91	2	-
GCF_900078335.1	s__Bordetella trematum	78.345	299	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
GCF_902859645.1	s__Achromobacter insuavis	78.344	368	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_017356245.1	s__Bordetella_A petrii_D	78.2467	336	1176	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_017745595.1	s__Bordetella_A petrii_C	78.2189	322	1176	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_002209565.1	s__Candidimonas nitroreducens	78.1654	222	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571365.1	s__Achromobacter denitrificans	78.1585	324	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_002209485.1	s__Bordetella_C sp002209485	78.1351	281	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009360345.1	s__Pigmentiphaga sp009360345	78.0179	224	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.85	99.84	0.97	0.96	3	-
GCF_019166065.1	s__Candidimonas humi	77.8877	238	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866805.1	s__Achromobacter_A aestuarii	77.7256	219	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894155.1	s__NBD-18 sp903894155	77.2685	152	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.08	98.85	0.85	0.83	4	-
GCA_903839085.1	s__Rhodoferax sp903839085	76.1994	78	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.74	99.66	0.90	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:55,713] [INFO] GTDB search result was written to GCF_003123725.1_ASM312372v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:55,713] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:55,721] [INFO] DFAST_QC result json was written to GCF_003123725.1_ASM312372v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:55,721] [INFO] DFAST_QC completed!
[2024-01-25 17:49:55,722] [INFO] Total running time: 0h1m35s