[2024-01-24 13:09:49,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,473] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference
[2024-01-24 13:09:50,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,788] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa9dbe06-aa80-42e1-8ce5-dd6c14ff5985/GCF_002233755.1_ASM223375v1_genomic.fna.gz | prodigal -d GCF_002233755.1_ASM223375v1_genomic.fna/cds.fna -a GCF_002233755.1_ASM223375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:58,560] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:58,561] [INFO] Task started: HMMsearch
[2024-01-24 13:09:58,561] [INFO] Running command: hmmsearch --tblout GCF_002233755.1_ASM223375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/reference_markers.hmm GCF_002233755.1_ASM223375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:58,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:58,833] [INFO] Found 6/6 markers.
[2024-01-24 13:09:58,869] [INFO] Query marker FASTA was written to GCF_002233755.1_ASM223375v1_genomic.fna/markers.fasta
[2024-01-24 13:09:58,869] [INFO] Task started: Blastn
[2024-01-24 13:09:58,869] [INFO] Running command: blastn -query GCF_002233755.1_ASM223375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/reference_markers.fasta -out GCF_002233755.1_ASM223375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:59,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:59,572] [INFO] Selected 13 target genomes.
[2024-01-24 13:09:59,572] [INFO] Target genome list was writen to GCF_002233755.1_ASM223375v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:59,595] [INFO] Task started: fastANI
[2024-01-24 13:09:59,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9dbe06-aa80-42e1-8ce5-dd6c14ff5985/GCF_002233755.1_ASM223375v1_genomic.fna.gz --refList GCF_002233755.1_ASM223375v1_genomic.fna/target_genomes.txt --output GCF_002233755.1_ASM223375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:10,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:10,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:10,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:10,073] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:10,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:10,074] [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 piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	100.0	1162	1165	95	conclusive
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	89.5981	971	1165	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	82.7255	763	1165	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	82.7162	762	1165	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	82.3893	736	1165	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	81.6582	724	1165	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	81.2147	637	1165	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	80.8529	605	1165	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.4106	566	1165	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.1284	472	1165	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.1723	386	1165	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.0877	327	1165	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.7825	377	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:10,075] [INFO] DFAST Taxonomy check result was written to GCF_002233755.1_ASM223375v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:10,076] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:10,076] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:10,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/checkm_data
[2024-01-24 13:10:10,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:10,115] [INFO] Task started: CheckM
[2024-01-24 13:10:10,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002233755.1_ASM223375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002233755.1_ASM223375v1_genomic.fna/checkm_input GCF_002233755.1_ASM223375v1_genomic.fna/checkm_result
[2024-01-24 13:10:39,123] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:39,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:39,143] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:39,143] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:39,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002233755.1_ASM223375v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:39,144] [INFO] Task started: Blastn
[2024-01-24 13:10:39,144] [INFO] Running command: blastn -query GCF_002233755.1_ASM223375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa244d92-b8bd-4f41-af44-6dd3ca3a1888/dqc_reference/reference_markers_gtdb.fasta -out GCF_002233755.1_ASM223375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:40,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:40,247] [INFO] Selected 10 target genomes.
[2024-01-24 13:10:40,247] [INFO] Target genome list was writen to GCF_002233755.1_ASM223375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:40,259] [INFO] Task started: fastANI
[2024-01-24 13:10:40,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9dbe06-aa80-42e1-8ce5-dd6c14ff5985/GCF_002233755.1_ASM223375v1_genomic.fna.gz --refList GCF_002233755.1_ASM223375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002233755.1_ASM223375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:49,427] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:49,440] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:49,440] [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_002233755.1	s__Acinetobacter piscicola	100.0	1162	1165	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_003611475.1	s__Acinetobacter rongchengensis	89.5981	971	1165	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	88.8085	947	1165	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	82.7292	763	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_001696605.3	s__Acinetobacter wuhouensis	82.4001	735	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	81.5018	688	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	81.2213	636	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015218165.1	s__Acinetobacter piscicola_A	81.121	643	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_002135415.1	s__Acinetobacter sp002135415	80.5842	668	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135235.1	s__Acinetobacter sp002135235	80.4106	566	1165	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 13:10:49,442] [INFO] GTDB search result was written to GCF_002233755.1_ASM223375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:49,442] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:49,445] [INFO] DFAST_QC result json was written to GCF_002233755.1_ASM223375v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:49,445] [INFO] DFAST_QC completed!
[2024-01-24 13:10:49,446] [INFO] Total running time: 0h0m60s