[2024-01-24 13:32:12,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:12,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:12,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference
[2024-01-24 13:32:13,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:13,620] [INFO] Task started: Prodigal
[2024-01-24 13:32:13,620] [INFO] Running command: gunzip -c /var/lib/cwl/stgcff81f78-ce2d-414d-a508-a824e0a2822f/GCF_004634245.1_ASM463424v1_genomic.fna.gz | prodigal -d GCF_004634245.1_ASM463424v1_genomic.fna/cds.fna -a GCF_004634245.1_ASM463424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:31,986] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:31,986] [INFO] Task started: HMMsearch
[2024-01-24 13:32:31,987] [INFO] Running command: hmmsearch --tblout GCF_004634245.1_ASM463424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/reference_markers.hmm GCF_004634245.1_ASM463424v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:32,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:32,287] [INFO] Found 6/6 markers.
[2024-01-24 13:32:32,329] [INFO] Query marker FASTA was written to GCF_004634245.1_ASM463424v1_genomic.fna/markers.fasta
[2024-01-24 13:32:32,329] [INFO] Task started: Blastn
[2024-01-24 13:32:32,330] [INFO] Running command: blastn -query GCF_004634245.1_ASM463424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/reference_markers.fasta -out GCF_004634245.1_ASM463424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:33,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:33,021] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:33,022] [INFO] Target genome list was writen to GCF_004634245.1_ASM463424v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:33,030] [INFO] Task started: fastANI
[2024-01-24 13:32:33,030] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff81f78-ce2d-414d-a508-a824e0a2822f/GCF_004634245.1_ASM463424v1_genomic.fna.gz --refList GCF_004634245.1_ASM463424v1_genomic.fna/target_genomes.txt --output GCF_004634245.1_ASM463424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:54,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:54,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:54,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:54,582] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:54,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:54,583] [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
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	100.0	1688	1690	95	conclusive
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	84.8064	1206	1690	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	84.6975	1193	1690	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	84.3461	1215	1690	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	83.6445	1049	1690	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	83.637	1013	1690	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	83.5767	1052	1690	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	83.536	1036	1690	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	83.456	1112	1690	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.4314	1159	1690	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	83.404	1089	1690	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	82.9851	1076	1690	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	82.8745	1052	1690	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.5226	973	1690	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	82.2722	925	1690	95	below_threshold
Flavobacterium ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	81.4343	918	1690	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.4374	141	1690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,591] [INFO] DFAST Taxonomy check result was written to GCF_004634245.1_ASM463424v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:54,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:54,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:54,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/checkm_data
[2024-01-24 13:32:54,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:54,652] [INFO] Task started: CheckM
[2024-01-24 13:32:54,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004634245.1_ASM463424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004634245.1_ASM463424v1_genomic.fna/checkm_input GCF_004634245.1_ASM463424v1_genomic.fna/checkm_result
[2024-01-24 13:33:51,626] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:51,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,647] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:51,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:51,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004634245.1_ASM463424v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:51,648] [INFO] Task started: Blastn
[2024-01-24 13:33:51,648] [INFO] Running command: blastn -query GCF_004634245.1_ASM463424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298c4500-3c60-4450-8a78-06db8cd09e80/dqc_reference/reference_markers_gtdb.fasta -out GCF_004634245.1_ASM463424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:52,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:52,613] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:52,613] [INFO] Target genome list was writen to GCF_004634245.1_ASM463424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:52,656] [INFO] Task started: fastANI
[2024-01-24 13:33:52,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff81f78-ce2d-414d-a508-a824e0a2822f/GCF_004634245.1_ASM463424v1_genomic.fna.gz --refList GCF_004634245.1_ASM463424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004634245.1_ASM463424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:13,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:13,593] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:13,594] [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_004634245.1	s__Flavobacterium foetidum	100.0	1688	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112575.1	s__Flavobacterium phragmitis	84.8031	1207	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393195.1	s__Flavobacterium collinsii_A	84.7118	1206	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122385.1	s__Flavobacterium crocinum	84.3256	1218	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	83.7034	1063	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	83.6829	1114	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101855.1	s__Flavobacterium anhuiense	83.6758	1068	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	83.633	1050	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003254545.1	s__Flavobacterium tistrianum	83.628	1014	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826975.1	s__Flavobacterium sp009826975	83.5694	1073	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	83.5365	1036	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	83.3966	1090	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	83.2318	1057	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312915.1	s__Flavobacterium sp003312915	82.9776	1077	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429295.1	s__Flavobacterium sp001429295	82.9643	1076	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_900129555.1	s__Flavobacterium defluvii	82.6232	951	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614725.1	s__Flavobacterium ajazii	81.4412	918	1690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,597] [INFO] GTDB search result was written to GCF_004634245.1_ASM463424v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:13,598] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:13,602] [INFO] DFAST_QC result json was written to GCF_004634245.1_ASM463424v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:13,602] [INFO] DFAST_QC completed!
[2024-01-24 13:34:13,602] [INFO] Total running time: 0h2m1s