[2024-01-24 12:54:22,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,027] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference
[2024-01-24 12:54:23,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,883] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg766da0be-af27-49f6-98e8-0f3dcf38f500/GCF_007988925.1_ASM798892v1_genomic.fna.gz | prodigal -d GCF_007988925.1_ASM798892v1_genomic.fna/cds.fna -a GCF_007988925.1_ASM798892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:33,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:33,912] [INFO] Task started: HMMsearch
[2024-01-24 12:54:33,912] [INFO] Running command: hmmsearch --tblout GCF_007988925.1_ASM798892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/reference_markers.hmm GCF_007988925.1_ASM798892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:34,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:34,191] [INFO] Found 6/6 markers.
[2024-01-24 12:54:34,225] [INFO] Query marker FASTA was written to GCF_007988925.1_ASM798892v1_genomic.fna/markers.fasta
[2024-01-24 12:54:34,226] [INFO] Task started: Blastn
[2024-01-24 12:54:34,226] [INFO] Running command: blastn -query GCF_007988925.1_ASM798892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/reference_markers.fasta -out GCF_007988925.1_ASM798892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:34,972] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:34,997] [INFO] Selected 20 target genomes.
[2024-01-24 12:54:34,997] [INFO] Target genome list was writen to GCF_007988925.1_ASM798892v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:35,008] [INFO] Task started: fastANI
[2024-01-24 12:54:35,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg766da0be-af27-49f6-98e8-0f3dcf38f500/GCF_007988925.1_ASM798892v1_genomic.fna.gz --refList GCF_007988925.1_ASM798892v1_genomic.fna/target_genomes.txt --output GCF_007988925.1_ASM798892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:47,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:47,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:47,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:47,328] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:47,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:47,329] [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
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	100.0	1146	1148	95	conclusive
Acidomonas methanolica	strain=DSM 5432	GCA_004346035.1	437	437	type	True	99.9976	1146	1148	95	conclusive
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	99.9482	1071	1148	95	conclusive
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	79.3393	360	1148	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	79.2117	336	1148	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.0702	350	1148	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	78.8857	370	1148	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	78.8535	371	1148	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.6863	328	1148	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.5279	239	1148	95	below_threshold
Tanticharoenia sakaeratensis	strain=NBRC 103193	GCA_000963885.1	444053	444053	type	True	78.4163	280	1148	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	78.2556	195	1148	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.25	198	1148	95	below_threshold
Kozakia baliensis	strain=DSM 14400	GCA_001787335.1	153496	153496	type	True	78.1928	216	1148	95	below_threshold
Kozakia baliensis	strain=NBRC 16664	GCA_007989365.1	153496	153496	type	True	78.1541	204	1148	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	78.0665	129	1148	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.9843	223	1148	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	77.7862	212	1148	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	77.7102	205	1148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:47,331] [INFO] DFAST Taxonomy check result was written to GCF_007988925.1_ASM798892v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:47,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:47,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:47,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/checkm_data
[2024-01-24 12:54:47,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:47,375] [INFO] Task started: CheckM
[2024-01-24 12:54:47,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007988925.1_ASM798892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007988925.1_ASM798892v1_genomic.fna/checkm_input GCF_007988925.1_ASM798892v1_genomic.fna/checkm_result
[2024-01-24 12:55:21,495] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:21,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:21,518] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:21,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:21,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007988925.1_ASM798892v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:21,519] [INFO] Task started: Blastn
[2024-01-24 12:55:21,519] [INFO] Running command: blastn -query GCF_007988925.1_ASM798892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a3f7f98-5f1d-400e-aa9d-123840600b6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007988925.1_ASM798892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:22,751] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:22,757] [INFO] Selected 23 target genomes.
[2024-01-24 12:55:22,758] [INFO] Target genome list was writen to GCF_007988925.1_ASM798892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:22,777] [INFO] Task started: fastANI
[2024-01-24 12:55:22,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg766da0be-af27-49f6-98e8-0f3dcf38f500/GCF_007988925.1_ASM798892v1_genomic.fna.gz --refList GCF_007988925.1_ASM798892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007988925.1_ASM798892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:36,472] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:36,495] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:36,495] [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_004346035.1	s__Acidomonas methanolica	99.9976	1146	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	conclusive
GCF_013376175.1	s__Ameyamaea chiangmaiensis	79.3831	246	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014174255.1	s__Gluconacetobacter sacchari	79.3781	401	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	79.3394	360	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.0696	349	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_002005465.1	s__Neoasaia chiangmaiensis	78.913	369	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014174375.1	s__Gluconacetobacter asukensis	78.8448	348	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174305.1	s__Gluconacetobacter johannae	78.8098	277	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.7674	319	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	78.6214	333	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	78.4521	328	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	78.2941	318	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_001787335.1	s__Kozakia baliensis	78.1943	216	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Kozakia	95.0	98.19	97.27	0.93	0.89	4	-
GCF_007988945.1	s__Swaminathania salitolerans	78.0487	261	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009547075.1	s__Gluconobacter sp009547075	77.969	224	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	77.9433	208	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_000614545.1	s__Asaia platycodi	77.8716	210	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	77.7102	205	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	77.5319	196	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:36,498] [INFO] GTDB search result was written to GCF_007988925.1_ASM798892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:36,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:36,502] [INFO] DFAST_QC result json was written to GCF_007988925.1_ASM798892v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:36,503] [INFO] DFAST_QC completed!
[2024-01-24 12:55:36,503] [INFO] Total running time: 0h1m14s