[2024-01-24 13:25:47,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,512] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference
[2024-01-24 13:25:48,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,892] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg7040babe-7b43-43c0-b24a-98f4ddad1020/GCF_000621065.1_ASM62106v1_genomic.fna.gz | prodigal -d GCF_000621065.1_ASM62106v1_genomic.fna/cds.fna -a GCF_000621065.1_ASM62106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:58,342] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:58,343] [INFO] Task started: HMMsearch
[2024-01-24 13:25:58,343] [INFO] Running command: hmmsearch --tblout GCF_000621065.1_ASM62106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/reference_markers.hmm GCF_000621065.1_ASM62106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:58,607] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:58,609] [INFO] Found 6/6 markers.
[2024-01-24 13:25:58,641] [INFO] Query marker FASTA was written to GCF_000621065.1_ASM62106v1_genomic.fna/markers.fasta
[2024-01-24 13:25:58,641] [INFO] Task started: Blastn
[2024-01-24 13:25:58,642] [INFO] Running command: blastn -query GCF_000621065.1_ASM62106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/reference_markers.fasta -out GCF_000621065.1_ASM62106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:59,350] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:59,354] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:59,354] [INFO] Target genome list was writen to GCF_000621065.1_ASM62106v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:59,362] [INFO] Task started: fastANI
[2024-01-24 13:25:59,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg7040babe-7b43-43c0-b24a-98f4ddad1020/GCF_000621065.1_ASM62106v1_genomic.fna.gz --refList GCF_000621065.1_ASM62106v1_genomic.fna/target_genomes.txt --output GCF_000621065.1_ASM62106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:12,187] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:12,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:12,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:12,202] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:12,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:12,203] [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 tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	100.0	1297	1306	95	conclusive
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	99.9757	1291	1306	95	conclusive
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	86.4548	934	1306	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.5258	560	1306	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	81.3925	571	1306	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	81.3866	543	1306	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	80.7243	487	1306	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	80.4658	450	1306	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	80.3529	484	1306	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	80.2461	471	1306	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.2054	488	1306	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	80.134	453	1306	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	79.8567	470	1306	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7666	435	1306	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.6926	441	1306	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	79.6781	448	1306	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.4262	391	1306	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.363	385	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,204] [INFO] DFAST Taxonomy check result was written to GCF_000621065.1_ASM62106v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:12,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:12,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:12,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/checkm_data
[2024-01-24 13:26:12,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:12,246] [INFO] Task started: CheckM
[2024-01-24 13:26:12,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621065.1_ASM62106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621065.1_ASM62106v1_genomic.fna/checkm_input GCF_000621065.1_ASM62106v1_genomic.fna/checkm_result
[2024-01-24 13:26:45,267] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:45,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,288] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:45,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:45,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621065.1_ASM62106v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:45,290] [INFO] Task started: Blastn
[2024-01-24 13:26:45,290] [INFO] Running command: blastn -query GCF_000621065.1_ASM62106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6c4449-8ca3-4f53-bf5b-0e38a8dbda8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621065.1_ASM62106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:46,351] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:46,355] [INFO] Selected 9 target genomes.
[2024-01-24 13:26:46,355] [INFO] Target genome list was writen to GCF_000621065.1_ASM62106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:46,362] [INFO] Task started: fastANI
[2024-01-24 13:26:46,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg7040babe-7b43-43c0-b24a-98f4ddad1020/GCF_000621065.1_ASM62106v1_genomic.fna.gz --refList GCF_000621065.1_ASM62106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621065.1_ASM62106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:54,021] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:54,033] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:54,034] [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_000400735.1	s__Acinetobacter tandoii	99.9757	1291	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	conclusive
GCF_003105055.1	s__Acinetobacter sp003105055	91.9667	982	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331175.1	s__Acinetobacter sp004331175	91.227	999	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331255.1	s__Acinetobacter sp004331255	91.0954	1000	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331035.1	s__Acinetobacter sp004331035	90.9256	1015	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939195.1	s__Acinetobacter kanungonis	86.4548	934	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_000368045.1	s__Acinetobacter johnsonii	81.495	572	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_002165305.2	s__Acinetobacter sp002165305	81.4858	590	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135205.1	s__Acinetobacter sp002135205	81.388	588	1306	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:54,035] [INFO] GTDB search result was written to GCF_000621065.1_ASM62106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:54,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:54,039] [INFO] DFAST_QC result json was written to GCF_000621065.1_ASM62106v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:54,039] [INFO] DFAST_QC completed!
[2024-01-24 13:26:54,039] [INFO] Total running time: 0h1m7s