[2024-01-24 11:44:23,568] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stge92f532e-91fc-411f-bc00-c9d49fdb7d48/GCF_025660375.1_ASM2566037v1_genomic.fna.gz | prodigal -d GCF_025660375.1_ASM2566037v1_genomic.fna/cds.fna -a GCF_025660375.1_ASM2566037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:32,601] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:32,602] [INFO] Task started: HMMsearch
[2024-01-24 11:44:32,602] [INFO] Running command: hmmsearch --tblout GCF_025660375.1_ASM2566037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/reference_markers.hmm GCF_025660375.1_ASM2566037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:32,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:32,896] [INFO] Found 6/6 markers.
[2024-01-24 11:44:32,923] [INFO] Query marker FASTA was written to GCF_025660375.1_ASM2566037v1_genomic.fna/markers.fasta
[2024-01-24 11:44:32,924] [INFO] Task started: Blastn
[2024-01-24 11:44:32,924] [INFO] Running command: blastn -query GCF_025660375.1_ASM2566037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/reference_markers.fasta -out GCF_025660375.1_ASM2566037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:33,531] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:33,535] [INFO] Selected 30 target genomes.
[2024-01-24 11:44:33,535] [INFO] Target genome list was writen to GCF_025660375.1_ASM2566037v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:33,578] [INFO] Task started: fastANI
[2024-01-24 11:44:33,579] [INFO] Running command: fastANI --query /var/lib/cwl/stge92f532e-91fc-411f-bc00-c9d49fdb7d48/GCF_025660375.1_ASM2566037v1_genomic.fna.gz --refList GCF_025660375.1_ASM2566037v1_genomic.fna/target_genomes.txt --output GCF_025660375.1_ASM2566037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:51,962] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:51,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:51,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:51,983] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:51,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:51,983] [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
Caldibacillus pasinlerensis	strain=P1	GCA_009996845.1	2703818	2703818	type	True	82.2608	593	1078	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	78.2745	203	1078	95	below_threshold
Bacillus kwashiorkori	strain=SIT6	GCA_001375515.1	1522318	1522318	type	True	77.7934	103	1078	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.4523	60	1078	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	76.8988	81	1078	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.7701	66	1078	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.6153	67	1078	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	76.456	68	1078	95	below_threshold
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	76.4298	50	1078	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	76.3783	60	1078	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	76.3473	62	1078	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	76.3473	62	1078	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	76.2722	73	1078	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	76.0407	70	1078	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	75.9757	71	1078	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	75.9212	69	1078	95	below_threshold
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	75.6242	59	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,985] [INFO] DFAST Taxonomy check result was written to GCF_025660375.1_ASM2566037v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:51,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:51,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:51,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/checkm_data
[2024-01-24 11:44:51,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:52,021] [INFO] Task started: CheckM
[2024-01-24 11:44:52,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025660375.1_ASM2566037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025660375.1_ASM2566037v1_genomic.fna/checkm_input GCF_025660375.1_ASM2566037v1_genomic.fna/checkm_result
[2024-01-24 11:45:17,076] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:17,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,092] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:17,092] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:17,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025660375.1_ASM2566037v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:17,093] [INFO] Task started: Blastn
[2024-01-24 11:45:17,094] [INFO] Running command: blastn -query GCF_025660375.1_ASM2566037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f804158-76e1-4a94-8d92-6f78ee8cc750/dqc_reference/reference_markers_gtdb.fasta -out GCF_025660375.1_ASM2566037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:17,919] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:17,923] [INFO] Selected 23 target genomes.
[2024-01-24 11:45:17,924] [INFO] Target genome list was writen to GCF_025660375.1_ASM2566037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:17,941] [INFO] Task started: fastANI
[2024-01-24 11:45:17,942] [INFO] Running command: fastANI --query /var/lib/cwl/stge92f532e-91fc-411f-bc00-c9d49fdb7d48/GCF_025660375.1_ASM2566037v1_genomic.fna.gz --refList GCF_025660375.1_ASM2566037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025660375.1_ASM2566037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:31,086] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:31,099] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:31,099] [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
GCA_902796085.1	s__RUG14133 sp902796085	99.0973	728	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__RUG14133	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009996845.1	s__RUG14133 sp009996845	82.243	593	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__RUG14133	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244735.1	s__Bacillus_J andreraoultii	78.3053	202	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_001375515.1	s__Bacillus_BK kwashiorkori	77.7934	103	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_BK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000751775.1	s__Bacillus_J thermoamylovorans	76.9589	155	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	98.31	97.86	0.86	0.85	9	-
GCF_016772275.1	s__Heyndrickxia vini	76.8697	82	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375675.1	s__Massilibacterium senegalense	76.7255	56	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_E;f__Massilibacteriaceae;g__Massilibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900217795.1	s__Ureibacillus xyleni	76.6728	55	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259935.1	s__Anoxybacillus_B vitaminiphilus	76.4842	67	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242895.2	s__Bacillus_BU sp000242895	76.4611	61	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273755.1	s__Peribacillus butanolivorans	76.3442	59	1078	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_003628435.1	s__Ureibacillus endophyticus	76.327	59	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	76.0111	57	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884235.1	s__Bacillus_A paramycoides	75.8881	63	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.72	97.18	0.88	0.85	10	-
GCA_012840465.1	s__Calidifontibacillus sp012840465	75.799	54	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307855.1	s__Calidifontibacillus azotoformans	75.6242	59	1078	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	97.05	97.05	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:31,101] [INFO] GTDB search result was written to GCF_025660375.1_ASM2566037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:31,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:31,105] [INFO] DFAST_QC result json was written to GCF_025660375.1_ASM2566037v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:31,106] [INFO] DFAST_QC completed!
[2024-01-24 11:45:31,106] [INFO] Total running time: 0h1m8s