[2024-01-24 15:10:20,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference
[2024-01-24 15:10:23,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,844] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg76d71d39-99e6-4514-8d36-36def0622812/GCF_001742425.1_ASM174242v1_genomic.fna.gz | prodigal -d GCF_001742425.1_ASM174242v1_genomic.fna/cds.fna -a GCF_001742425.1_ASM174242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:31,114] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:31,114] [INFO] Task started: HMMsearch
[2024-01-24 15:10:31,114] [INFO] Running command: hmmsearch --tblout GCF_001742425.1_ASM174242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/reference_markers.hmm GCF_001742425.1_ASM174242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:31,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:31,361] [INFO] Found 6/6 markers.
[2024-01-24 15:10:31,390] [INFO] Query marker FASTA was written to GCF_001742425.1_ASM174242v1_genomic.fna/markers.fasta
[2024-01-24 15:10:31,390] [INFO] Task started: Blastn
[2024-01-24 15:10:31,390] [INFO] Running command: blastn -query GCF_001742425.1_ASM174242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/reference_markers.fasta -out GCF_001742425.1_ASM174242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:32,041] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:32,050] [INFO] Selected 29 target genomes.
[2024-01-24 15:10:32,050] [INFO] Target genome list was writen to GCF_001742425.1_ASM174242v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:32,078] [INFO] Task started: fastANI
[2024-01-24 15:10:32,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d71d39-99e6-4514-8d36-36def0622812/GCF_001742425.1_ASM174242v1_genomic.fna.gz --refList GCF_001742425.1_ASM174242v1_genomic.fna/target_genomes.txt --output GCF_001742425.1_ASM174242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:52,812] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:52,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:52,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:52,847] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:52,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:52,847] [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
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	100.0	1241	1247	95	conclusive
Calidifontibacillus oryziterrae	strain=ZYK	GCA_000331575.1	1191699	1191699	type	True	76.832	65	1247	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.6861	74	1247	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.5611	67	1247	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.56	78	1247	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	76.5541	52	1247	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	76.5526	68	1247	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	76.5422	70	1247	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	76.4921	79	1247	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.4167	78	1247	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	76.3882	74	1247	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.3684	86	1247	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.3304	68	1247	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.3097	75	1247	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	76.2071	86	1247	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	76.2039	62	1247	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.1882	90	1247	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	76.1646	89	1247	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	76.1213	81	1247	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	76.0757	66	1247	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.0164	63	1247	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	75.9761	91	1247	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	75.6306	86	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:52,861] [INFO] DFAST Taxonomy check result was written to GCF_001742425.1_ASM174242v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:52,862] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:52,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:52,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/checkm_data
[2024-01-24 15:10:52,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:52,945] [INFO] Task started: CheckM
[2024-01-24 15:10:52,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001742425.1_ASM174242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001742425.1_ASM174242v1_genomic.fna/checkm_input GCF_001742425.1_ASM174242v1_genomic.fna/checkm_result
[2024-01-24 15:11:21,248] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:21,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:21,271] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:21,271] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:21,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001742425.1_ASM174242v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:21,272] [INFO] Task started: Blastn
[2024-01-24 15:11:21,272] [INFO] Running command: blastn -query GCF_001742425.1_ASM174242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e384529-9ff0-48a4-85c8-96e0ef8df037/dqc_reference/reference_markers_gtdb.fasta -out GCF_001742425.1_ASM174242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:22,124] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:22,128] [INFO] Selected 29 target genomes.
[2024-01-24 15:11:22,128] [INFO] Target genome list was writen to GCF_001742425.1_ASM174242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:22,147] [INFO] Task started: fastANI
[2024-01-24 15:11:22,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d71d39-99e6-4514-8d36-36def0622812/GCF_001742425.1_ASM174242v1_genomic.fna.gz --refList GCF_001742425.1_ASM174242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001742425.1_ASM174242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:42,805] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:42,822] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:42,822] [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_001742425.1	s__Bacillus_AV solimangrovi	100.0	1241	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003184905.1	s__Priestia sp003184905	76.8808	83	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	76.6861	74	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_002835735.1	s__Cytobacillus horneckiae	76.6406	68	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_002276165.1	s__Cytobacillus kochii	76.5048	75	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262935.1	s__Lottiidibacillus patelloidae	76.4485	74	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_E;f__SA5d-4;g__Lottiidibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002560985.1	s__Bacillus_A sp002560985	76.3385	98	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837155.1	s__Litchfieldia sp014837155	76.3321	85	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836495.1	s__Cytobacillus sp014836495	76.3073	69	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577195.1	s__Gottfriedia sp002577195	76.2886	74	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814275.1	s__Gottfriedia sp017814275	76.2801	72	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	76.2232	76	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183415.1	s__Niallia sp009183415	76.2083	69	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908395.1	s__Metabacillus crassostreae	76.1718	87	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001883995.1	s__Bacillus_A paranthracis	76.1646	89	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	97.40	95.70	0.86	0.80	231	-
GCF_002551005.1	s__Bacillus_A pseudomycoides_C	76.141	89	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156875.1	s__Gottfriedia sp002156875	76.1345	78	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285535.1	s__Fredinandcohnia timonensis	76.0646	85	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112415.1	s__Bacillus_A sp900112415	76.0125	101	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.00	99.00	0.93	0.93	2	-
GCF_002250055.1	s__Sutcliffiella cohnii	75.9761	91	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_000981385.1	s__Metabacillus sp000981385	75.87	68	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638355.1	s__Priestia_D taiwanensis	75.7727	68	1247	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Priestia_D	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:42,825] [INFO] GTDB search result was written to GCF_001742425.1_ASM174242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:42,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:42,833] [INFO] DFAST_QC result json was written to GCF_001742425.1_ASM174242v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:42,833] [INFO] DFAST_QC completed!
[2024-01-24 15:11:42,834] [INFO] Total running time: 0h1m23s