[2024-01-24 13:12:38,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference
[2024-01-24 13:12:39,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:39,920] [INFO] Task started: Prodigal
[2024-01-24 13:12:39,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg44a107b0-969d-4bac-b424-73e5ddd74d34/GCF_002723955.1_ASM272395v1_genomic.fna.gz | prodigal -d GCF_002723955.1_ASM272395v1_genomic.fna/cds.fna -a GCF_002723955.1_ASM272395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:49,910] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:49,911] [INFO] Task started: HMMsearch
[2024-01-24 13:12:49,911] [INFO] Running command: hmmsearch --tblout GCF_002723955.1_ASM272395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/reference_markers.hmm GCF_002723955.1_ASM272395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:50,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:50,304] [INFO] Found 6/6 markers.
[2024-01-24 13:12:50,345] [INFO] Query marker FASTA was written to GCF_002723955.1_ASM272395v1_genomic.fna/markers.fasta
[2024-01-24 13:12:50,345] [INFO] Task started: Blastn
[2024-01-24 13:12:50,345] [INFO] Running command: blastn -query GCF_002723955.1_ASM272395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/reference_markers.fasta -out GCF_002723955.1_ASM272395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:51,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:51,161] [INFO] Selected 12 target genomes.
[2024-01-24 13:12:51,161] [INFO] Target genome list was writen to GCF_002723955.1_ASM272395v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:51,170] [INFO] Task started: fastANI
[2024-01-24 13:12:51,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg44a107b0-969d-4bac-b424-73e5ddd74d34/GCF_002723955.1_ASM272395v1_genomic.fna.gz --refList GCF_002723955.1_ASM272395v1_genomic.fna/target_genomes.txt --output GCF_002723955.1_ASM272395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:59,496] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:59,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:59,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:59,506] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:12:59,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:59,507] [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 frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	100.0	1097	1098	95	conclusive
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	89.7128	875	1098	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	89.648	878	1098	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	88.0604	780	1098	95	below_threshold
Gluconobacter cerinus	strain=NBRC 3267	GCA_002723935.1	38307	38307	type	True	83.5156	658	1098	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	79.8679	434	1098	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	79.6867	426	1098	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	79.6404	406	1098	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	79.4936	377	1098	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.1755	143	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:59,509] [INFO] DFAST Taxonomy check result was written to GCF_002723955.1_ASM272395v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:59,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:59,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:59,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/checkm_data
[2024-01-24 13:12:59,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:59,548] [INFO] Task started: CheckM
[2024-01-24 13:12:59,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002723955.1_ASM272395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002723955.1_ASM272395v1_genomic.fna/checkm_input GCF_002723955.1_ASM272395v1_genomic.fna/checkm_result
[2024-01-24 13:13:33,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:33,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:33,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:33,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:33,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002723955.1_ASM272395v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:33,406] [INFO] Task started: Blastn
[2024-01-24 13:13:33,407] [INFO] Running command: blastn -query GCF_002723955.1_ASM272395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7df223c-952d-45c5-ab3e-d5f0255da165/dqc_reference/reference_markers_gtdb.fasta -out GCF_002723955.1_ASM272395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:34,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:34,635] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:34,635] [INFO] Target genome list was writen to GCF_002723955.1_ASM272395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:34,642] [INFO] Task started: fastANI
[2024-01-24 13:13:34,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg44a107b0-969d-4bac-b424-73e5ddd74d34/GCF_002723955.1_ASM272395v1_genomic.fna.gz --refList GCF_002723955.1_ASM272395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002723955.1_ASM272395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:41,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:41,036] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:41,036] [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_002723955.1	s__Gluconobacter_A frateurii	100.0	1097	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	conclusive
GCF_000964465.1	s__Gluconobacter_A thailandicus	89.6627	877	1098	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_002723975.1	s__Gluconobacter_A japonicus	88.0604	780	1098	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_002723935.1	s__Gluconobacter_A cerinus	83.5156	658	1098	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_014132155.1	s__Gluconobacter_A sp014132155	83.4808	629	1098	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_015244565.1	s__Gluconobacter vitians	79.8777	404	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	79.758	393	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_015244675.1	s__Gluconobacter cerevisiae	79.6903	378	1098	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	79.6867	426	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000234355.1	s__Gluconobacter_C morbifer	79.5062	376	1098	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 13:13:41,039] [INFO] GTDB search result was written to GCF_002723955.1_ASM272395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:41,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:41,044] [INFO] DFAST_QC result json was written to GCF_002723955.1_ASM272395v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:41,044] [INFO] DFAST_QC completed!
[2024-01-24 13:13:41,044] [INFO] Total running time: 0h1m3s