[2024-01-24 11:43:42,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference
[2024-01-24 11:43:43,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,725] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg549b1f9f-7d7c-4416-83d1-34542e84bc7c/GCF_025995135.1_ASM2599513v1_genomic.fna.gz | prodigal -d GCF_025995135.1_ASM2599513v1_genomic.fna/cds.fna -a GCF_025995135.1_ASM2599513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:53,729] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:53,729] [INFO] Task started: HMMsearch
[2024-01-24 11:43:53,730] [INFO] Running command: hmmsearch --tblout GCF_025995135.1_ASM2599513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/reference_markers.hmm GCF_025995135.1_ASM2599513v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,072] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,073] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,130] [INFO] Query marker FASTA was written to GCF_025995135.1_ASM2599513v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,131] [INFO] Task started: Blastn
[2024-01-24 11:43:54,131] [INFO] Running command: blastn -query GCF_025995135.1_ASM2599513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/reference_markers.fasta -out GCF_025995135.1_ASM2599513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:54,884] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:54,891] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:54,892] [INFO] Target genome list was writen to GCF_025995135.1_ASM2599513v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:54,897] [INFO] Task started: fastANI
[2024-01-24 11:43:54,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg549b1f9f-7d7c-4416-83d1-34542e84bc7c/GCF_025995135.1_ASM2599513v1_genomic.fna.gz --refList GCF_025995135.1_ASM2599513v1_genomic.fna/target_genomes.txt --output GCF_025995135.1_ASM2599513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:03,558] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:03,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:03,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:03,569] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:03,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:03,570] [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 thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	99.9871	1064	1097	95	conclusive
Gluconobacter thailandicus	strain=NBRC 100600	GCA_007990185.1	257438	257438	type	True	99.9805	1067	1097	95	conclusive
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	89.782	882	1097	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	87.0264	785	1097	95	below_threshold
Gluconobacter cerinus	strain=NBRC 3267	GCA_002723935.1	38307	38307	type	True	83.4626	645	1097	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	80.1635	442	1097	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	79.4857	421	1097	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	79.4466	414	1097	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	79.2769	386	1097	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.6091	110	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:03,571] [INFO] DFAST Taxonomy check result was written to GCF_025995135.1_ASM2599513v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:03,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:03,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:03,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/checkm_data
[2024-01-24 11:44:03,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:03,614] [INFO] Task started: CheckM
[2024-01-24 11:44:03,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995135.1_ASM2599513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995135.1_ASM2599513v1_genomic.fna/checkm_input GCF_025995135.1_ASM2599513v1_genomic.fna/checkm_result
[2024-01-24 11:44:38,220] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:38,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,242] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:38,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:38,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995135.1_ASM2599513v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:38,243] [INFO] Task started: Blastn
[2024-01-24 11:44:38,243] [INFO] Running command: blastn -query GCF_025995135.1_ASM2599513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51726e82-d7bb-44a9-9a10-44ced7d693db/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995135.1_ASM2599513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,429] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,459] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:39,459] [INFO] Target genome list was writen to GCF_025995135.1_ASM2599513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:39,505] [INFO] Task started: fastANI
[2024-01-24 11:44:39,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg549b1f9f-7d7c-4416-83d1-34542e84bc7c/GCF_025995135.1_ASM2599513v1_genomic.fna.gz --refList GCF_025995135.1_ASM2599513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995135.1_ASM2599513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:46,460] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:46,476] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:46,477] [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_000964465.1	s__Gluconobacter_A thailandicus	99.9871	1064	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	conclusive
GCF_002723955.1	s__Gluconobacter_A frateurii	89.782	882	1097	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_002723975.1	s__Gluconobacter_A japonicus	87.0136	786	1097	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_014132155.1	s__Gluconobacter_A sp014132155	83.6513	648	1097	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	83.4903	643	1097	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_001580675.1	s__Gluconobacter potus	79.996	437	1097	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	79.8267	405	1097	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	79.4912	420	1097	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	79.2769	386	1097	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_000613885.1	s__Asaia prunellae	77.302	107	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:46,478] [INFO] GTDB search result was written to GCF_025995135.1_ASM2599513v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:46,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:46,483] [INFO] DFAST_QC result json was written to GCF_025995135.1_ASM2599513v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:46,484] [INFO] DFAST_QC completed!
[2024-01-24 11:44:46,484] [INFO] Total running time: 0h1m4s