[2024-01-24 13:58:55,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference
[2024-01-24 13:58:57,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,394] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,394] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9361b9d-bc3a-46e3-8797-31690ee7e6f7/GCF_030160135.1_ASM3016013v1_genomic.fna.gz | prodigal -d GCF_030160135.1_ASM3016013v1_genomic.fna/cds.fna -a GCF_030160135.1_ASM3016013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:06,441] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:06,442] [INFO] Task started: HMMsearch
[2024-01-24 13:59:06,442] [INFO] Running command: hmmsearch --tblout GCF_030160135.1_ASM3016013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/reference_markers.hmm GCF_030160135.1_ASM3016013v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:06,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:06,714] [INFO] Found 6/6 markers.
[2024-01-24 13:59:06,750] [INFO] Query marker FASTA was written to GCF_030160135.1_ASM3016013v1_genomic.fna/markers.fasta
[2024-01-24 13:59:06,750] [INFO] Task started: Blastn
[2024-01-24 13:59:06,751] [INFO] Running command: blastn -query GCF_030160135.1_ASM3016013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/reference_markers.fasta -out GCF_030160135.1_ASM3016013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,526] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:07,527] [INFO] Target genome list was writen to GCF_030160135.1_ASM3016013v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:07,553] [INFO] Task started: fastANI
[2024-01-24 13:59:07,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9361b9d-bc3a-46e3-8797-31690ee7e6f7/GCF_030160135.1_ASM3016013v1_genomic.fna.gz --refList GCF_030160135.1_ASM3016013v1_genomic.fna/target_genomes.txt --output GCF_030160135.1_ASM3016013v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:16,424] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:16,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:16,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:16,438] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:16,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:16,439] [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
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	99.9907	989	1019	95	conclusive
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	87.9084	783	1019	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	86.875	789	1019	95	below_threshold
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	86.8076	805	1019	95	below_threshold
Gluconobacter cerinus	strain=NBRC 3267	GCA_002723935.1	38307	38307	type	True	82.8687	638	1019	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	80.2416	410	1019	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	80.1802	413	1019	95	below_threshold
Gluconobacter cerevisiae	strain=DSM 27644	GCA_018811965.1	1379734	1379734	type	True	79.8758	393	1019	95	below_threshold
Gluconobacter cerevisiae	strain=LMG 27748	GCA_015244675.1	1379734	1379734	type	True	79.8472	396	1019	95	below_threshold
Gluconobacter kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	79.6742	356	1019	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	79.2029	360	1019	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	77.7545	121	1019	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.2483	96	1019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:16,441] [INFO] DFAST Taxonomy check result was written to GCF_030160135.1_ASM3016013v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:16,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:16,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:16,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/checkm_data
[2024-01-24 13:59:16,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:16,475] [INFO] Task started: CheckM
[2024-01-24 13:59:16,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160135.1_ASM3016013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160135.1_ASM3016013v1_genomic.fna/checkm_input GCF_030160135.1_ASM3016013v1_genomic.fna/checkm_result
[2024-01-24 13:59:47,754] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:47,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,776] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:47,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:47,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160135.1_ASM3016013v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:47,776] [INFO] Task started: Blastn
[2024-01-24 13:59:47,777] [INFO] Running command: blastn -query GCF_030160135.1_ASM3016013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb46d5f5-297f-456e-be64-8ed5592b4a30/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160135.1_ASM3016013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:49,073] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:49,077] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:49,077] [INFO] Target genome list was writen to GCF_030160135.1_ASM3016013v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:49,094] [INFO] Task started: fastANI
[2024-01-24 13:59:49,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9361b9d-bc3a-46e3-8797-31690ee7e6f7/GCF_030160135.1_ASM3016013v1_genomic.fna.gz --refList GCF_030160135.1_ASM3016013v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160135.1_ASM3016013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:56,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:56,426] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:56,427] [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_002723975.1	s__Gluconobacter_A japonicus	99.9907	989	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.84	95.27	0.89	0.85	9	conclusive
GCF_002723955.1	s__Gluconobacter_A frateurii	87.9253	782	1019	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_000964465.1	s__Gluconobacter_A thailandicus	86.8624	790	1019	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_014132155.1	s__Gluconobacter_A sp014132155	83.0179	626	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.46	96.68	0.90	0.89	4	-
GCF_002723935.1	s__Gluconobacter_A cerinus	82.8552	640	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.40	95.61	0.88	0.86	20	-
GCF_009547075.1	s__Gluconobacter sp009547075	80.2334	411	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580675.1	s__Gluconobacter potus	80.1986	415	1019	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	79.8507	395	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006538885.1	s__Gluconobacter roseus	79.8153	402	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007988905.1	s__Gluconobacter kanchanaburiensis	79.6888	355	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000234355.1	s__Gluconobacter_C morbifer	79.216	359	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:56,429] [INFO] GTDB search result was written to GCF_030160135.1_ASM3016013v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:56,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:56,434] [INFO] DFAST_QC result json was written to GCF_030160135.1_ASM3016013v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:56,434] [INFO] DFAST_QC completed!
[2024-01-24 13:59:56,434] [INFO] Total running time: 0h1m0s