[2024-01-24 14:23:20,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference
[2024-01-24 14:23:21,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,911] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,912] [INFO] Running command: gunzip -c /var/lib/cwl/stg752ad958-0b1f-4014-be87-29aab36ddc04/GCF_006542335.1_ASM654233v1_genomic.fna.gz | prodigal -d GCF_006542335.1_ASM654233v1_genomic.fna/cds.fna -a GCF_006542335.1_ASM654233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:29,499] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:29,499] [INFO] Task started: HMMsearch
[2024-01-24 14:23:29,499] [INFO] Running command: hmmsearch --tblout GCF_006542335.1_ASM654233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/reference_markers.hmm GCF_006542335.1_ASM654233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:29,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:29,817] [INFO] Found 6/6 markers.
[2024-01-24 14:23:29,843] [INFO] Query marker FASTA was written to GCF_006542335.1_ASM654233v1_genomic.fna/markers.fasta
[2024-01-24 14:23:29,843] [INFO] Task started: Blastn
[2024-01-24 14:23:29,844] [INFO] Running command: blastn -query GCF_006542335.1_ASM654233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/reference_markers.fasta -out GCF_006542335.1_ASM654233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:30,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:30,625] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:30,626] [INFO] Target genome list was writen to GCF_006542335.1_ASM654233v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:30,634] [INFO] Task started: fastANI
[2024-01-24 14:23:30,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg752ad958-0b1f-4014-be87-29aab36ddc04/GCF_006542335.1_ASM654233v1_genomic.fna.gz --refList GCF_006542335.1_ASM654233v1_genomic.fna/target_genomes.txt --output GCF_006542335.1_ASM654233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:40,555] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:40,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:40,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:40,565] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:40,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:40,566] [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
Neokomagataea tanensis	strain=AH13 = NBRC 106556	GCA_006542335.1	661191	661191	type	True	100.0	855	858	95	conclusive
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	80.4773	371	858	95	below_threshold
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	80.2169	373	858	95	below_threshold
Swingsia samuiensis	strain=AH83	GCA_006542355.1	1293412	1293412	type	True	78.8374	74	858	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	78.0883	102	858	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	78.0697	88	858	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	78.0595	105	858	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	77.9605	102	858	95	below_threshold
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	77.9107	103	858	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	77.8947	102	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:40,567] [INFO] DFAST Taxonomy check result was written to GCF_006542335.1_ASM654233v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:40,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:40,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:40,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/checkm_data
[2024-01-24 14:23:40,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:40,598] [INFO] Task started: CheckM
[2024-01-24 14:23:40,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542335.1_ASM654233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542335.1_ASM654233v1_genomic.fna/checkm_input GCF_006542335.1_ASM654233v1_genomic.fna/checkm_result
[2024-01-24 14:24:10,634] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:10,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:10,655] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:10,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:10,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542335.1_ASM654233v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:10,656] [INFO] Task started: Blastn
[2024-01-24 14:24:10,656] [INFO] Running command: blastn -query GCF_006542335.1_ASM654233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b8fddfe-5a65-4d3b-8fe0-c76480825e78/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542335.1_ASM654233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:11,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:11,800] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:11,800] [INFO] Target genome list was writen to GCF_006542335.1_ASM654233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:11,835] [INFO] Task started: fastANI
[2024-01-24 14:24:11,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg752ad958-0b1f-4014-be87-29aab36ddc04/GCF_006542335.1_ASM654233v1_genomic.fna.gz --refList GCF_006542335.1_ASM654233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006542335.1_ASM654233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:19,658] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:19,675] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:19,675] [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_006542335.1	s__Neokomagataea tanensis	100.0	857	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018122595.1	s__Neokomagataea sp018122595	80.4773	371	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598495.1	s__Neokomagataea thailandica	80.2214	373	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542355.1	s__Swingsia samuiensis	78.8863	78	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swingsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723975.1	s__Gluconobacter_A japonicus	78.0883	102	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.84	95.27	0.89	0.85	9	-
GCF_002723955.1	s__Gluconobacter_A frateurii	78.0595	105	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
GCF_000234355.1	s__Gluconobacter_C morbifer	78.0564	89	858	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_015244745.1	s__Gluconobacter cadivus	77.9605	102	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
GCF_000964465.1	s__Gluconobacter_A thailandicus	77.8947	102	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	-
GCF_001580675.1	s__Gluconobacter potus	77.7585	91	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_015244675.1	s__Gluconobacter cerevisiae	77.724	96	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:19,677] [INFO] GTDB search result was written to GCF_006542335.1_ASM654233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:19,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:19,681] [INFO] DFAST_QC result json was written to GCF_006542335.1_ASM654233v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:19,681] [INFO] DFAST_QC completed!
[2024-01-24 14:24:19,681] [INFO] Total running time: 0h0m59s