[2024-01-24 12:42:08,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:08,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:08,887] [INFO] DQC Reference Directory: /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference
[2024-01-24 12:42:10,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,228] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e380538-5989-4c13-97a8-b74b32e8fcd4/GCF_000430245.1_Acinetobacter_gerneri_genomic.fna.gz | prodigal -d GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/cds.fna -a GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:19,765] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:19,766] [INFO] Task started: HMMsearch
[2024-01-24 12:42:19,766] [INFO] Running command: hmmsearch --tblout GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/reference_markers.hmm GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:20,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:20,082] [INFO] Found 6/6 markers.
[2024-01-24 12:42:20,125] [INFO] Query marker FASTA was written to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/markers.fasta
[2024-01-24 12:42:20,125] [INFO] Task started: Blastn
[2024-01-24 12:42:20,125] [INFO] Running command: blastn -query GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/markers.fasta -db /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/reference_markers.fasta -out GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:20,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:20,863] [INFO] Selected 17 target genomes.
[2024-01-24 12:42:20,864] [INFO] Target genome list was writen to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/target_genomes.txt
[2024-01-24 12:42:20,870] [INFO] Task started: fastANI
[2024-01-24 12:42:20,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e380538-5989-4c13-97a8-b74b32e8fcd4/GCF_000430245.1_Acinetobacter_gerneri_genomic.fna.gz --refList GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/target_genomes.txt --output GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:34,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:34,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:34,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:34,383] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:42:34,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:34,383] [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=MTCC 9824	GCA_000430245.1	202952	202952	type	True	100.0	1385	1392	95	conclusive
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	99.9669	1385	1392	95	conclusive
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	99.9514	1323	1392	95	conclusive
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	81.3026	625	1392	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.4888	569	1392	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.2859	555	1392	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.0714	413	1392	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	79.8641	518	1392	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	79.8279	574	1392	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	79.8152	580	1392	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.734	407	1392	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7169	462	1392	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.358	369	1392	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	79.3565	403	1392	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.1882	316	1392	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.1378	381	1392	95	below_threshold
Acinetobacter nosocomialis	strain=NIPH 2119	GCA_000368085.1	106654	106654	type	True	79.1284	403	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:34,385] [INFO] DFAST Taxonomy check result was written to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/tc_result.tsv
[2024-01-24 12:42:34,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:34,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:34,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/checkm_data
[2024-01-24 12:42:34,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:34,439] [INFO] Task started: CheckM
[2024-01-24 12:42:34,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/checkm_input GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/checkm_result
[2024-01-24 12:43:08,687] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:08,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:08,711] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:08,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:08,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/markers.fasta)
[2024-01-24 12:43:08,712] [INFO] Task started: Blastn
[2024-01-24 12:43:08,712] [INFO] Running command: blastn -query GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/markers.fasta -db /var/lib/cwl/stga4a2e2bf-31cf-4cfa-a276-6745fa796011/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:09,810] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:09,815] [INFO] Selected 21 target genomes.
[2024-01-24 12:43:09,815] [INFO] Target genome list was writen to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:09,866] [INFO] Task started: fastANI
[2024-01-24 12:43:09,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e380538-5989-4c13-97a8-b74b32e8fcd4/GCF_000430245.1_Acinetobacter_gerneri_genomic.fna.gz --refList GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/target_genomes_gtdb.txt --output GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:25,617] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:25,640] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:25,640] [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	99.9669	1385	1392	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	81.3153	623	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_001696605.3	s__Acinetobacter wuhouensis	80.4919	568	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_015218165.1	s__Acinetobacter piscicola_A	80.3586	577	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_000214135.1	s__Acinetobacter sp000214135	80.2444	523	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	80.0505	415	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_902809855.1	s__Acinetobacter sp902809855	79.9423	542	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368925.1	s__Acinetobacter bereziniae	79.8585	519	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_002135415.1	s__Acinetobacter sp002135415	79.8549	551	1392	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	79.8492	573	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_009707625.1	s__Acinetobacter sp009707625	79.7842	395	1392	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	79.7313	391	1392	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	79.6725	423	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.6449	482	1392	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	79.6367	488	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.90	99.88	0.97	0.96	14	-
GCF_003024525.3	s__Acinetobacter cumulans	79.6094	406	1392	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	79.5701	394	1392	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	79.3963	426	1392	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	79.3514	403	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009759685.1	s__Acinetobacter baumannii	79.2032	380	1392	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	79.117	404	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:25,643] [INFO] GTDB search result was written to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:25,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:25,647] [INFO] DFAST_QC result json was written to GCF_000430245.1_Acinetobacter_gerneri_genomic.fna/dqc_result.json
[2024-01-24 12:43:25,648] [INFO] DFAST_QC completed!
[2024-01-24 12:43:25,648] [INFO] Total running time: 0h1m17s