[2024-01-24 13:36:45,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference
[2024-01-24 13:36:46,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,786] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg01513f47-eb35-4782-a340-ce6bba16ba1e/GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna.gz | prodigal -d GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/cds.fna -a GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:57,063] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:57,064] [INFO] Task started: HMMsearch
[2024-01-24 13:36:57,064] [INFO] Running command: hmmsearch --tblout GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/reference_markers.hmm GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:57,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:57,390] [INFO] Found 6/6 markers.
[2024-01-24 13:36:57,431] [INFO] Query marker FASTA was written to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/markers.fasta
[2024-01-24 13:36:57,432] [INFO] Task started: Blastn
[2024-01-24 13:36:57,432] [INFO] Running command: blastn -query GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/reference_markers.fasta -out GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:58,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:58,154] [INFO] Selected 17 target genomes.
[2024-01-24 13:36:58,155] [INFO] Target genome list was writen to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:58,164] [INFO] Task started: fastANI
[2024-01-24 13:36:58,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg01513f47-eb35-4782-a340-ce6bba16ba1e/GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna.gz --refList GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/target_genomes.txt --output GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:13,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:13,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:13,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:13,767] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:13,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:13,767] [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
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	99.9911	1488	1511	95	conclusive
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	99.9077	1362	1511	95	conclusive
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	99.9071	1383	1511	95	conclusive
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	81.3864	637	1511	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.7619	580	1511	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.3182	564	1511	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.2767	408	1511	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.1975	437	1511	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	80.0118	537	1511	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	80.0066	591	1511	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	79.8885	581	1511	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7813	463	1511	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	79.7616	411	1511	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.6885	396	1511	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.6432	381	1511	95	below_threshold
Acinetobacter nosocomialis	strain=NIPH 2119	GCA_000368085.1	106654	106654	type	True	79.5582	396	1511	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.1894	327	1511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:13,769] [INFO] DFAST Taxonomy check result was written to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:13,769] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:13,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:13,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/checkm_data
[2024-01-24 13:37:13,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:13,817] [INFO] Task started: CheckM
[2024-01-24 13:37:13,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/checkm_input GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/checkm_result
[2024-01-24 13:37:50,316] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:50,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,335] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:50,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:50,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/markers.fasta)
[2024-01-24 13:37:50,336] [INFO] Task started: Blastn
[2024-01-24 13:37:50,337] [INFO] Running command: blastn -query GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7980b0f-e383-483b-b454-a075e47e5149/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:51,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:51,444] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:51,444] [INFO] Target genome list was writen to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:51,498] [INFO] Task started: fastANI
[2024-01-24 13:37:51,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg01513f47-eb35-4782-a340-ce6bba16ba1e/GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna.gz --refList GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:08,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:08,639] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:08,640] [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_000368565.1	s__Acinetobacter gerneri	99.9911	1487	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	conclusive
GCF_900323515.1	s__Acinetobacter stercoris	81.4038	639	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_015218165.1	s__Acinetobacter piscicola_A	80.6926	604	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_001696605.3	s__Acinetobacter wuhouensis	80.6801	581	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_009372215.1	s__Acinetobacter portensis	80.2489	410	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_000214135.1	s__Acinetobacter sp000214135	80.2298	537	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	80.1243	543	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	80.0565	588	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_000368925.1	s__Acinetobacter bereziniae	80.004	538	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_009707625.1	s__Acinetobacter sp009707625	79.9831	408	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336635.1	s__Acinetobacter sp004336635	79.9606	435	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_003024525.3	s__Acinetobacter cumulans	79.9412	432	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_002135355.1	s__Acinetobacter sp002135355	79.8483	398	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135415.1	s__Acinetobacter sp002135415	79.8441	570	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135315.1	s__Acinetobacter sp002135315	79.7523	404	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307195.1	s__Acinetobacter equi	79.7461	412	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508585.1	s__Acinetobacter baumannii_B	79.7022	498	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.90	99.88	0.97	0.96	14	-
GCF_009759685.1	s__Acinetobacter baumannii	79.6999	378	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	-
GCF_000368085.1	s__Acinetobacter nosocomialis	79.6345	399	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.6182	512	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135335.1	s__Acinetobacter sp002135335	79.4127	445	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:08,642] [INFO] GTDB search result was written to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:08,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:08,650] [INFO] DFAST_QC result json was written to GCF_000368565.1_Acin_gern_CIP_107464_V1_genomic.fna/dqc_result.json
[2024-01-24 13:38:08,650] [INFO] DFAST_QC completed!
[2024-01-24 13:38:08,651] [INFO] Total running time: 0h1m23s