[2024-01-24 12:30:52,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference
[2024-01-24 12:30:53,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,665] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f63c77e-7d37-43db-8b33-5d79ebda3595/GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna.gz | prodigal -d GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/cds.fna -a GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:02,588] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:02,588] [INFO] Task started: HMMsearch
[2024-01-24 12:31:02,589] [INFO] Running command: hmmsearch --tblout GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/reference_markers.hmm GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:02,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:02,887] [INFO] Found 6/6 markers.
[2024-01-24 12:31:02,933] [INFO] Query marker FASTA was written to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/markers.fasta
[2024-01-24 12:31:02,933] [INFO] Task started: Blastn
[2024-01-24 12:31:02,934] [INFO] Running command: blastn -query GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/reference_markers.fasta -out GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,662] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,666] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:03,666] [INFO] Target genome list was writen to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:03,679] [INFO] Task started: fastANI
[2024-01-24 12:31:03,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f63c77e-7d37-43db-8b33-5d79ebda3595/GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna.gz --refList GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/target_genomes.txt --output GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:19,998] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:19,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:19,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:20,020] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:20,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:20,020] [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 rudis	strain=CIP 110305	GCA_000413895.1	632955	632955	type	True	99.9945	1335	1350	95	conclusive
Acinetobacter rudis	strain=DSM 24031	GCA_000829675.1	632955	632955	type	True	99.9255	1233	1350	95	conclusive
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	79.2897	323	1350	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.2345	275	1350	95	below_threshold
Acinetobacter pullicarnis	strain=S23	GCA_006352475.1	2576829	2576829	type	True	79.2092	416	1350	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	79.0685	346	1350	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	79.0462	374	1350	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	79.0196	369	1350	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	78.9467	356	1350	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	78.9278	367	1350	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	78.9276	314	1350	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	78.9022	331	1350	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.897	357	1350	95	below_threshold
Acinetobacter lanii	strain=185	GCA_011578285.1	2715163	2715163	type	True	78.8899	294	1350	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	78.8568	344	1350	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	78.7994	309	1350	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.7612	311	1350	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.7074	338	1350	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	78.6422	315	1350	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	78.5431	298	1350	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	78.4487	306	1350	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.4481	259	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:20,021] [INFO] DFAST Taxonomy check result was written to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:20,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:20,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:20,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/checkm_data
[2024-01-24 12:31:20,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:20,064] [INFO] Task started: CheckM
[2024-01-24 12:31:20,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/checkm_input GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/checkm_result
[2024-01-24 12:31:51,920] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:51,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,944] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:51,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:51,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/markers.fasta)
[2024-01-24 12:31:51,945] [INFO] Task started: Blastn
[2024-01-24 12:31:51,945] [INFO] Running command: blastn -query GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbbc204-6c49-4839-84b7-13ab356fc56e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:53,022] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:53,027] [INFO] Selected 25 target genomes.
[2024-01-24 12:31:53,027] [INFO] Target genome list was writen to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:53,049] [INFO] Task started: fastANI
[2024-01-24 12:31:53,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f63c77e-7d37-43db-8b33-5d79ebda3595/GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna.gz --refList GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:10,064] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:10,085] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:10,085] [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_000829675.1	s__Acinetobacter rudis	99.9255	1233	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000367925.1	s__Acinetobacter bohemicus	79.2882	324	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_001696605.3	s__Acinetobacter wuhouensis	79.2167	352	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_004345325.1	s__Acinetobacter calcoaceticus_D	79.1871	385	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352475.1	s__Acinetobacter pullicarnis	79.1783	416	1350	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	79.0336	373	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_003024515.2	s__Acinetobacter sichuanensis	79.0197	369	1350	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	78.9577	366	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	78.9306	265	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011578285.1	s__Acinetobacter lanii	78.9246	293	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.20	97.20	0.92	0.92	2	-
GCF_001704615.3	s__Acinetobacter defluvii	78.9226	355	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.60	97.60	0.89	0.89	2	-
GCF_000400735.1	s__Acinetobacter tandoii	78.9089	331	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_000400715.1	s__Acinetobacter sp000400715	78.8795	311	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	78.8774	359	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368785.1	s__Acinetobacter towneri	78.8481	319	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_009707625.1	s__Acinetobacter sp009707625	78.8331	285	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002233755.1	s__Acinetobacter piscicola	78.8283	346	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008993995.1	s__Acinetobacter brisouii_A	78.7374	243	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCF_003268395.1	s__Acinetobacter sp003268395	78.7359	358	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369505.1	s__Acinetobacter sp000369505	78.7105	273	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_004336635.1	s__Acinetobacter sp004336635	78.7032	309	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_002135235.1	s__Acinetobacter sp002135235	78.6802	340	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753255.1	s__Acinetobacter sp011753255	78.554	302	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758345.1	s__Acinetobacter towneri_A	78.535	304	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.24	97.24	0.85	0.85	2	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	78.4414	306	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,087] [INFO] GTDB search result was written to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:10,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:10,092] [INFO] DFAST_QC result json was written to GCF_000413895.1_Acin_rudi_CIP_110305_V1_genomic.fna/dqc_result.json
[2024-01-24 12:32:10,092] [INFO] DFAST_QC completed!
[2024-01-24 12:32:10,092] [INFO] Total running time: 0h1m18s