[2024-01-24 13:17:34,702] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference
[2024-01-24 13:17:36,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,115] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg96c3b681-ad7b-433e-ae69-bd80a3519787/GCF_002165375.2_ASM216537v2_genomic.fna.gz | prodigal -d GCF_002165375.2_ASM216537v2_genomic.fna/cds.fna -a GCF_002165375.2_ASM216537v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:44,897] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:44,898] [INFO] Task started: HMMsearch
[2024-01-24 13:17:44,898] [INFO] Running command: hmmsearch --tblout GCF_002165375.2_ASM216537v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/reference_markers.hmm GCF_002165375.2_ASM216537v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,168] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,199] [INFO] Query marker FASTA was written to GCF_002165375.2_ASM216537v2_genomic.fna/markers.fasta
[2024-01-24 13:17:45,199] [INFO] Task started: Blastn
[2024-01-24 13:17:45,200] [INFO] Running command: blastn -query GCF_002165375.2_ASM216537v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/reference_markers.fasta -out GCF_002165375.2_ASM216537v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:45,908] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:45,912] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:45,912] [INFO] Target genome list was writen to GCF_002165375.2_ASM216537v2_genomic.fna/target_genomes.txt
[2024-01-24 13:17:45,920] [INFO] Task started: fastANI
[2024-01-24 13:17:45,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c3b681-ad7b-433e-ae69-bd80a3519787/GCF_002165375.2_ASM216537v2_genomic.fna.gz --refList GCF_002165375.2_ASM216537v2_genomic.fna/target_genomes.txt --output GCF_002165375.2_ASM216537v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:02,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:02,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,648] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:02,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:02,648] [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 chinensis	strain=WCHAc010005	GCA_002165375.2	2004650	2004650	type	True	100.0	1240	1243	95	conclusive
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	83.3547	570	1243	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	81.4011	475	1243	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.9	462	1243	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.487	428	1243	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	80.3459	418	1243	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	80.2872	465	1243	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	80.2175	466	1243	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	80.1537	481	1243	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	80.1157	454	1243	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	80.079	449	1243	95	below_threshold
Acinetobacter bouvetii	strain=CIP 107468	GCA_000368865.1	202951	202951	type	True	80.07	444	1243	95	below_threshold
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	80.042	436	1243	95	below_threshold
Acinetobacter terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	80.0201	481	1243	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.8784	459	1243	95	below_threshold
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	79.8232	451	1243	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.8117	393	1243	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7464	376	1243	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.5937	446	1243	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.4456	321	1243	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.4362	306	1243	95	below_threshold
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	79.4268	386	1243	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.3225	319	1243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,650] [INFO] DFAST Taxonomy check result was written to GCF_002165375.2_ASM216537v2_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/checkm_data
[2024-01-24 13:18:02,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,691] [INFO] Task started: CheckM
[2024-01-24 13:18:02,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002165375.2_ASM216537v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002165375.2_ASM216537v2_genomic.fna/checkm_input GCF_002165375.2_ASM216537v2_genomic.fna/checkm_result
[2024-01-24 13:18:37,167] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:37,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:37,187] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:37,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:37,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002165375.2_ASM216537v2_genomic.fna/markers.fasta)
[2024-01-24 13:18:37,188] [INFO] Task started: Blastn
[2024-01-24 13:18:37,189] [INFO] Running command: blastn -query GCF_002165375.2_ASM216537v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e5c2072-17f4-4b6b-8f85-4a53e9be3910/dqc_reference/reference_markers_gtdb.fasta -out GCF_002165375.2_ASM216537v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:38,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:38,390] [INFO] Selected 21 target genomes.
[2024-01-24 13:18:38,390] [INFO] Target genome list was writen to GCF_002165375.2_ASM216537v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:38,411] [INFO] Task started: fastANI
[2024-01-24 13:18:38,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg96c3b681-ad7b-433e-ae69-bd80a3519787/GCF_002165375.2_ASM216537v2_genomic.fna.gz --refList GCF_002165375.2_ASM216537v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002165375.2_ASM216537v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:55,418] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,435] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:55,436] [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_002165375.2	s__Acinetobacter chinensis	100.0	1239	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.92	0.89	0.89	2	conclusive
GCF_001696605.3	s__Acinetobacter wuhouensis	83.3514	570	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_003268395.1	s__Acinetobacter sp003268395	82.2878	474	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704615.3	s__Acinetobacter defluvii	81.3101	472	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.60	97.60	0.89	0.89	2	-
GCF_003024515.2	s__Acinetobacter sichuanensis	80.9222	461	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647675.1	s__Acinetobacter sp001647675	80.8026	382	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678755.1	s__Acinetobacter gandensis	80.4821	427	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_002135355.1	s__Acinetobacter sp002135355	80.3946	492	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	80.3863	490	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369625.1	s__Acinetobacter variabilis	80.2886	464	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.2563	491	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000488255.1	s__Acinetobacter indicus	80.1878	482	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCF_002135295.1	s__Acinetobacter sp002135295	80.1556	433	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611475.1	s__Acinetobacter rongchengensis	80.1537	451	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004375.1	s__Acinetobacter terrae	80.1462	467	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_000214135.1	s__Acinetobacter sp000214135	80.1434	433	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.1274	450	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.0345	437	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_004331155.1	s__Acinetobacter terrestris	79.9765	485	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCA_002455755.1	s__Acinetobacter sp002455755	79.8256	400	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.84	0.75	0.75	2	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.6045	428	1243	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 13:18:55,437] [INFO] GTDB search result was written to GCF_002165375.2_ASM216537v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:55,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:55,443] [INFO] DFAST_QC result json was written to GCF_002165375.2_ASM216537v2_genomic.fna/dqc_result.json
[2024-01-24 13:18:55,443] [INFO] DFAST_QC completed!
[2024-01-24 13:18:55,443] [INFO] Total running time: 0h1m21s