[2024-01-24 11:12:56,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:56,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:56,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference
[2024-01-24 11:12:57,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:57,860] [INFO] Task started: Prodigal
[2024-01-24 11:12:57,861] [INFO] Running command: gunzip -c /var/lib/cwl/stge99ced3e-069d-4877-84e9-f865b0bb09d6/GCF_000292245.2_ASM29224v2_genomic.fna.gz | prodigal -d GCF_000292245.2_ASM29224v2_genomic.fna/cds.fna -a GCF_000292245.2_ASM29224v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:06,172] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:06,172] [INFO] Task started: HMMsearch
[2024-01-24 11:13:06,173] [INFO] Running command: hmmsearch --tblout GCF_000292245.2_ASM29224v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/reference_markers.hmm GCF_000292245.2_ASM29224v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:06,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:06,509] [INFO] Found 6/6 markers.
[2024-01-24 11:13:06,560] [INFO] Query marker FASTA was written to GCF_000292245.2_ASM29224v2_genomic.fna/markers.fasta
[2024-01-24 11:13:06,560] [INFO] Task started: Blastn
[2024-01-24 11:13:06,561] [INFO] Running command: blastn -query GCF_000292245.2_ASM29224v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/reference_markers.fasta -out GCF_000292245.2_ASM29224v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:07,196] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:07,200] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:07,200] [INFO] Target genome list was writen to GCF_000292245.2_ASM29224v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:07,274] [INFO] Task started: fastANI
[2024-01-24 11:13:07,274] [INFO] Running command: fastANI --query /var/lib/cwl/stge99ced3e-069d-4877-84e9-f865b0bb09d6/GCF_000292245.2_ASM29224v2_genomic.fna.gz --refList GCF_000292245.2_ASM29224v2_genomic.fna/target_genomes.txt --output GCF_000292245.2_ASM29224v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:23,543] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:23,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:23,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:23,555] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:23,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:23,556] [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
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	100.0	1363	1372	95	conclusive
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	99.8503	1172	1372	95	conclusive
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	81.3177	205	1372	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	78.1797	251	1372	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	78.1566	268	1372	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	77.2115	158	1372	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	77.1131	82	1372	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	77.0342	95	1372	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	76.999	90	1372	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	76.8664	82	1372	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.5202	118	1372	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	76.4708	53	1372	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.3836	62	1372	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.3413	60	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,557] [INFO] DFAST Taxonomy check result was written to GCF_000292245.2_ASM29224v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:23,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:23,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:23,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/checkm_data
[2024-01-24 11:13:23,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:23,604] [INFO] Task started: CheckM
[2024-01-24 11:13:23,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000292245.2_ASM29224v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000292245.2_ASM29224v2_genomic.fna/checkm_input GCF_000292245.2_ASM29224v2_genomic.fna/checkm_result
[2024-01-24 11:13:54,800] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:54,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:54,824] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:54,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:54,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000292245.2_ASM29224v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:54,825] [INFO] Task started: Blastn
[2024-01-24 11:13:54,825] [INFO] Running command: blastn -query GCF_000292245.2_ASM29224v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg521368f3-d44e-46bb-94ea-b2093410939f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000292245.2_ASM29224v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:55,608] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:55,611] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:55,611] [INFO] Target genome list was writen to GCF_000292245.2_ASM29224v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:55,625] [INFO] Task started: fastANI
[2024-01-24 11:13:55,625] [INFO] Running command: fastANI --query /var/lib/cwl/stge99ced3e-069d-4877-84e9-f865b0bb09d6/GCF_000292245.2_ASM29224v2_genomic.fna.gz --refList GCF_000292245.2_ASM29224v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000292245.2_ASM29224v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:11,273] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:11,289] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:11,290] [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_000292245.2	s__Alkalihalobacillus alcalophilus	100.0	1363	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	conclusive
GCF_000787375.1	s__Bacillus_L okhensis	81.3177	205	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	78.6542	426	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590785.1	s__Alkalihalobacillus trypoxylicola	78.1872	269	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	-
GCF_002156385.1	s__45385 sp002156385	77.5617	156	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	77.4003	130	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797325.1	s__Bacillus_S sp002797325	77.3566	126	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745675.1	s__Bacillus_BH sp017745675	77.2431	117	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	77.0942	80	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.0604	71	1372	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_002019795.1	s__Bacillus_AO alkalicellulosilyticus	77.0533	96	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363695.1	s__Sutcliffiella_A sp009363695	76.8974	57	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	76.8664	82	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003184905.1	s__Priestia sp003184905	76.7847	86	1372	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_019024285.1	s__Bacillus_BH sp019024285	76.5152	117	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273755.1	s__Peribacillus butanolivorans	76.4708	53	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.70	97.35	0.87	0.86	10	-
GCF_000380245.2	s__Bacillus_AD massiliogorillae	76.297	59	1372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:11,291] [INFO] GTDB search result was written to GCF_000292245.2_ASM29224v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:11,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:11,295] [INFO] DFAST_QC result json was written to GCF_000292245.2_ASM29224v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:11,295] [INFO] DFAST_QC completed!
[2024-01-24 11:14:11,295] [INFO] Total running time: 0h1m15s