[2024-01-25 18:46:05,701] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:05,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:05,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference
[2024-01-25 18:46:06,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:06,887] [INFO] Task started: Prodigal
[2024-01-25 18:46:06,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg2134f69c-712f-41f9-a36e-0737fa92adcc/GCF_003815775.1_ASM381577v1_genomic.fna.gz | prodigal -d GCF_003815775.1_ASM381577v1_genomic.fna/cds.fna -a GCF_003815775.1_ASM381577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:21,731] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:21,731] [INFO] Task started: HMMsearch
[2024-01-25 18:46:21,731] [INFO] Running command: hmmsearch --tblout GCF_003815775.1_ASM381577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/reference_markers.hmm GCF_003815775.1_ASM381577v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:21,980] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:21,984] [INFO] Found 6/6 markers.
[2024-01-25 18:46:22,028] [INFO] Query marker FASTA was written to GCF_003815775.1_ASM381577v1_genomic.fna/markers.fasta
[2024-01-25 18:46:22,028] [INFO] Task started: Blastn
[2024-01-25 18:46:22,028] [INFO] Running command: blastn -query GCF_003815775.1_ASM381577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/reference_markers.fasta -out GCF_003815775.1_ASM381577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:22,633] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:22,637] [INFO] Selected 14 target genomes.
[2024-01-25 18:46:22,637] [INFO] Target genome list was writen to GCF_003815775.1_ASM381577v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:22,654] [INFO] Task started: fastANI
[2024-01-25 18:46:22,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg2134f69c-712f-41f9-a36e-0737fa92adcc/GCF_003815775.1_ASM381577v1_genomic.fna.gz --refList GCF_003815775.1_ASM381577v1_genomic.fna/target_genomes.txt --output GCF_003815775.1_ASM381577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:37,723] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:37,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:37,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:37,733] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:46:37,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:37,733] [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
Chryseobacterium joostei	strain=DSM 16927	GCA_003815775.1	112234	112234	type	True	100.0	1627	1630	95	conclusive
Chryseobacterium joostei	strain=DSM 16927	GCA_900156585.1	112234	112234	type	True	99.9897	1603	1630	95	conclusive
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	93.9746	1339	1630	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	91.22	1318	1630	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	84.3431	1142	1630	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.1279	1103	1630	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	84.0146	1156	1630	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.9009	1058	1630	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	83.5197	1077	1630	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4593	681	1630	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.3548	750	1630	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3544	696	1630	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.2763	513	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:37,734] [INFO] DFAST Taxonomy check result was written to GCF_003815775.1_ASM381577v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:37,735] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:37,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:37,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/checkm_data
[2024-01-25 18:46:37,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:37,783] [INFO] Task started: CheckM
[2024-01-25 18:46:37,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003815775.1_ASM381577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003815775.1_ASM381577v1_genomic.fna/checkm_input GCF_003815775.1_ASM381577v1_genomic.fna/checkm_result
[2024-01-25 18:47:22,932] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:22,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:22,998] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:22,998] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:22,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003815775.1_ASM381577v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:22,999] [INFO] Task started: Blastn
[2024-01-25 18:47:22,999] [INFO] Running command: blastn -query GCF_003815775.1_ASM381577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7adadd6-7210-4fc0-9fb7-be9bba7f8434/dqc_reference/reference_markers_gtdb.fasta -out GCF_003815775.1_ASM381577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:23,877] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:23,879] [INFO] Selected 10 target genomes.
[2024-01-25 18:47:23,879] [INFO] Target genome list was writen to GCF_003815775.1_ASM381577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:23,890] [INFO] Task started: fastANI
[2024-01-25 18:47:23,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg2134f69c-712f-41f9-a36e-0737fa92adcc/GCF_003815775.1_ASM381577v1_genomic.fna.gz --refList GCF_003815775.1_ASM381577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003815775.1_ASM381577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:36,087] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:36,094] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:36,094] [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_003815775.1	s__Chryseobacterium joostei	100.0	1626	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.33	98.66	0.96	0.94	3	conclusive
GCF_002899895.1	s__Chryseobacterium oncorhynchi	93.9761	1339	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	91.2328	1317	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815675.1	s__Chryseobacterium sp003815675	87.2194	1306	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	84.6063	1139	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829375.1	s__Chryseobacterium sp000829375	84.2634	1180	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684975.1	s__Chryseobacterium artocarpi	84.1414	1101	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	83.9938	1151	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900078205.2	s__Chryseobacterium timonianum	83.9119	1131	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274625.1	s__Chryseobacterium sp008274625	83.5168	1077	1630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:36,097] [INFO] GTDB search result was written to GCF_003815775.1_ASM381577v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:36,097] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:36,100] [INFO] DFAST_QC result json was written to GCF_003815775.1_ASM381577v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:36,100] [INFO] DFAST_QC completed!
[2024-01-25 18:47:36,101] [INFO] Total running time: 0h1m30s