[2024-01-24 14:14:47,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference
[2024-01-24 14:14:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,423] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stga7e53679-8e96-4c08-a3ca-d6f840c30c4c/GCF_006542375.1_ASM654237v1_genomic.fna.gz | prodigal -d GCF_006542375.1_ASM654237v1_genomic.fna/cds.fna -a GCF_006542375.1_ASM654237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:55,331] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:55,331] [INFO] Task started: HMMsearch
[2024-01-24 14:14:55,331] [INFO] Running command: hmmsearch --tblout GCF_006542375.1_ASM654237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/reference_markers.hmm GCF_006542375.1_ASM654237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:55,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:55,586] [INFO] Found 6/6 markers.
[2024-01-24 14:14:55,615] [INFO] Query marker FASTA was written to GCF_006542375.1_ASM654237v1_genomic.fna/markers.fasta
[2024-01-24 14:14:55,616] [INFO] Task started: Blastn
[2024-01-24 14:14:55,616] [INFO] Running command: blastn -query GCF_006542375.1_ASM654237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/reference_markers.fasta -out GCF_006542375.1_ASM654237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:57,201] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:57,204] [INFO] Selected 30 target genomes.
[2024-01-24 14:14:57,205] [INFO] Target genome list was writen to GCF_006542375.1_ASM654237v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:57,373] [INFO] Task started: fastANI
[2024-01-24 14:14:57,373] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e53679-8e96-4c08-a3ca-d6f840c30c4c/GCF_006542375.1_ASM654237v1_genomic.fna.gz --refList GCF_006542375.1_ASM654237v1_genomic.fna/target_genomes.txt --output GCF_006542375.1_ASM654237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:12,528] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:12,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:12,551] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:12,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:12,552] [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
Oecophyllibacter saccharovorans	strain=Ha5	GCA_006542375.1	2558360	2558360	type	True	100.0	647	648	95	conclusive
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	77.2499	124	648	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	77.1986	113	648	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	77.1553	126	648	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	77.1273	98	648	95	below_threshold
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	77.1256	122	648	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_002005465.1	320497	320497	type	True	77.0755	97	648	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	77.0407	115	648	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	77.012	125	648	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	76.9827	129	648	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	76.8914	128	648	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	76.8673	95	648	95	below_threshold
Neoasaia chiangmaiensis	strain=NBRC 101099	GCA_007991115.1	320497	320497	type	True	76.8534	96	648	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	76.8063	123	648	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	76.8057	106	648	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	76.782	123	648	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	76.771	100	648	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	76.7547	89	648	95	below_threshold
Gluconobacter wancherniae	strain=NBRC 103581	GCA_020884775.1	1307955	1307955	type	True	76.7527	67	648	95	below_threshold
Gluconobacter wancherniae	strain=LMG27016	GCA_015244585.1	1307955	1307955	type	True	76.7519	67	648	95	below_threshold
Gluconobacter wancherniae	strain=NBRC 103581	GCA_007988885.1	1307955	1307955	type	True	76.7519	67	648	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	76.7391	104	648	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	76.73	122	648	95	below_threshold
Acidomonas methanolica	strain=MB58	GCA_000617865.1	437	437	type	True	76.6889	103	648	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	76.625	105	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,553] [INFO] DFAST Taxonomy check result was written to GCF_006542375.1_ASM654237v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:12,554] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:12,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:12,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/checkm_data
[2024-01-24 14:15:12,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:12,578] [INFO] Task started: CheckM
[2024-01-24 14:15:12,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542375.1_ASM654237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542375.1_ASM654237v1_genomic.fna/checkm_input GCF_006542375.1_ASM654237v1_genomic.fna/checkm_result
[2024-01-24 14:15:35,830] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:35,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:35,852] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:35,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:35,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542375.1_ASM654237v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:35,853] [INFO] Task started: Blastn
[2024-01-24 14:15:35,853] [INFO] Running command: blastn -query GCF_006542375.1_ASM654237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f04bb92-0cbb-4c80-93b9-0d1818fc5f28/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542375.1_ASM654237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:37,143] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:37,146] [INFO] Selected 24 target genomes.
[2024-01-24 14:15:37,146] [INFO] Target genome list was writen to GCF_006542375.1_ASM654237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:37,170] [INFO] Task started: fastANI
[2024-01-24 14:15:37,170] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e53679-8e96-4c08-a3ca-d6f840c30c4c/GCF_006542375.1_ASM654237v1_genomic.fna.gz --refList GCF_006542375.1_ASM654237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006542375.1_ASM654237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:49,306] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:49,328] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:49,329] [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_006542375.1	s__Oecophyllibacter saccharovorans	100.0	647	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Oecophyllibacter	95.0	97.69	97.59	0.98	0.98	3	conclusive
GCF_018221685.1	s__Bombella apis	77.245	125	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048465.1	s__Bombella mellum	77.2011	124	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723915.1	s__Gluconobacter albidus	77.1591	99	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_014635085.1	s__Asaia siamensis	77.1452	101	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	77.1298	128	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_000234355.1	s__Gluconobacter_C morbifer	77.1224	99	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005465.1	s__Neoasaia chiangmaiensis	77.071	98	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neoasaia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	77.0599	115	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.0288	107	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	77.009	126	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014174255.1	s__Gluconacetobacter sacchari	76.9463	93	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285295.1	s__Komagataeibacter europaeus	76.927	108	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_000964425.1	s__Komagataeibacter intermedius	76.9221	99	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	76.9172	119	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244565.1	s__Gluconobacter vitians	76.8914	128	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	76.8622	96	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009547075.1	s__Gluconobacter sp009547075	76.8063	123	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018811945.1	s__Gluconobacter sp018811945	76.7994	127	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155395.1	s__Komagataeibacter melomenusus	76.7809	124	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_007988885.1	s__Gluconobacter_B wancherniae	76.7519	67	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_B	95.0	99.01	98.51	0.95	0.90	4	-
GCF_003207895.1	s__Komagataeibacter swingsii	76.748	122	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_004346035.1	s__Acidomonas methanolica	76.719	107	648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:49,330] [INFO] GTDB search result was written to GCF_006542375.1_ASM654237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:49,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:49,336] [INFO] DFAST_QC result json was written to GCF_006542375.1_ASM654237v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:49,336] [INFO] DFAST_QC completed!
[2024-01-24 14:15:49,336] [INFO] Total running time: 0h1m2s