[2024-01-25 18:14:05,734] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference
[2024-01-25 18:14:06,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,854] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,855] [INFO] Running command: gunzip -c /var/lib/cwl/stge7f32855-5d56-4563-817e-dba7a1ddb2f6/GCF_009707625.1_ASM970762v1_genomic.fna.gz | prodigal -d GCF_009707625.1_ASM970762v1_genomic.fna/cds.fna -a GCF_009707625.1_ASM970762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:11,357] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:11,358] [INFO] Task started: HMMsearch
[2024-01-25 18:14:11,358] [INFO] Running command: hmmsearch --tblout GCF_009707625.1_ASM970762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/reference_markers.hmm GCF_009707625.1_ASM970762v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:11,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:11,565] [INFO] Found 6/6 markers.
[2024-01-25 18:14:11,588] [INFO] Query marker FASTA was written to GCF_009707625.1_ASM970762v1_genomic.fna/markers.fasta
[2024-01-25 18:14:11,589] [INFO] Task started: Blastn
[2024-01-25 18:14:11,589] [INFO] Running command: blastn -query GCF_009707625.1_ASM970762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/reference_markers.fasta -out GCF_009707625.1_ASM970762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:12,274] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:12,279] [INFO] Selected 20 target genomes.
[2024-01-25 18:14:12,279] [INFO] Target genome list was writen to GCF_009707625.1_ASM970762v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:12,301] [INFO] Task started: fastANI
[2024-01-25 18:14:12,301] [INFO] Running command: fastANI --query /var/lib/cwl/stge7f32855-5d56-4563-817e-dba7a1ddb2f6/GCF_009707625.1_ASM970762v1_genomic.fna.gz --refList GCF_009707625.1_ASM970762v1_genomic.fna/target_genomes.txt --output GCF_009707625.1_ASM970762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:25,134] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:25,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:25,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:25,147] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:25,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:25,148] [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 portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	87.4232	677	836	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	81.533	518	836	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.1012	490	836	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	81.0894	468	836	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	81.0015	488	836	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.9409	461	836	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	80.9319	494	836	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	80.905	425	836	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	80.7398	442	836	95	below_threshold
Acinetobacter shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	80.7195	435	836	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.6041	481	836	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.4986	368	836	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.4372	456	836	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.3837	422	836	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.3404	419	836	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	80.325	417	836	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	80.1784	440	836	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.8625	426	836	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.3608	330	836	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.1636	334	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:25,152] [INFO] DFAST Taxonomy check result was written to GCF_009707625.1_ASM970762v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:25,152] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:25,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:25,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/checkm_data
[2024-01-25 18:14:25,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:25,184] [INFO] Task started: CheckM
[2024-01-25 18:14:25,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707625.1_ASM970762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707625.1_ASM970762v1_genomic.fna/checkm_input GCF_009707625.1_ASM970762v1_genomic.fna/checkm_result
[2024-01-25 18:14:44,634] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:44,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:44,672] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:44,673] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:44,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707625.1_ASM970762v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:44,673] [INFO] Task started: Blastn
[2024-01-25 18:14:44,673] [INFO] Running command: blastn -query GCF_009707625.1_ASM970762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg884df781-dad2-48be-9b36-33e054587ea9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707625.1_ASM970762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:45,762] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:45,764] [INFO] Selected 17 target genomes.
[2024-01-25 18:14:45,765] [INFO] Target genome list was writen to GCF_009707625.1_ASM970762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:45,790] [INFO] Task started: fastANI
[2024-01-25 18:14:45,790] [INFO] Running command: fastANI --query /var/lib/cwl/stge7f32855-5d56-4563-817e-dba7a1ddb2f6/GCF_009707625.1_ASM970762v1_genomic.fna.gz --refList GCF_009707625.1_ASM970762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707625.1_ASM970762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:57,254] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:57,265] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:57,265] [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_009707625.1	s__Acinetobacter sp009707625	100.0	832	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009372215.1	s__Acinetobacter portensis	87.4136	678	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_001307195.1	s__Acinetobacter equi	81.533	518	836	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	81.2061	459	836	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	81.1137	476	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_003664645.1	s__Acinetobacter chengduensis	81.0757	469	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_001678755.1	s__Acinetobacter gandensis	80.9819	487	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_009557235.1	s__Acinetobacter wanghuae	80.8863	426	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCF_002135295.1	s__Acinetobacter sp002135295	80.8701	457	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711395.1	s__Acinetobacter sp003711395	80.7351	402	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.7181	420	836	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	80.701	464	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_000632455.1	s__Acinetobacter sp000632455	80.646	383	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.93	97.36	0.88	0.86	4	-
GCF_013004375.1	s__Acinetobacter terrae	80.5911	482	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_001707755.1	s__Acinetobacter celticus	80.442	456	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268395.1	s__Acinetobacter sp003268395	80.2455	424	836	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	79.8145	398	836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:57,267] [INFO] GTDB search result was written to GCF_009707625.1_ASM970762v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:57,267] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:57,270] [INFO] DFAST_QC result json was written to GCF_009707625.1_ASM970762v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:57,270] [INFO] DFAST_QC completed!
[2024-01-25 18:14:57,270] [INFO] Total running time: 0h0m52s