[2024-01-24 13:01:38,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference
[2024-01-24 13:01:40,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,906] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d5ec182-4628-4eaf-a934-0e89b48f840d/GCF_009996845.1_ASM999684v1_genomic.fna.gz | prodigal -d GCF_009996845.1_ASM999684v1_genomic.fna/cds.fna -a GCF_009996845.1_ASM999684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:46,441] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:46,441] [INFO] Task started: HMMsearch
[2024-01-24 13:01:46,441] [INFO] Running command: hmmsearch --tblout GCF_009996845.1_ASM999684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/reference_markers.hmm GCF_009996845.1_ASM999684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:46,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:46,749] [INFO] Found 6/6 markers.
[2024-01-24 13:01:46,779] [INFO] Query marker FASTA was written to GCF_009996845.1_ASM999684v1_genomic.fna/markers.fasta
[2024-01-24 13:01:46,779] [INFO] Task started: Blastn
[2024-01-24 13:01:46,780] [INFO] Running command: blastn -query GCF_009996845.1_ASM999684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/reference_markers.fasta -out GCF_009996845.1_ASM999684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:47,773] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:47,778] [INFO] Selected 35 target genomes.
[2024-01-24 13:01:47,778] [INFO] Target genome list was writen to GCF_009996845.1_ASM999684v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:47,797] [INFO] Task started: fastANI
[2024-01-24 13:01:47,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5ec182-4628-4eaf-a934-0e89b48f840d/GCF_009996845.1_ASM999684v1_genomic.fna.gz --refList GCF_009996845.1_ASM999684v1_genomic.fna/target_genomes.txt --output GCF_009996845.1_ASM999684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:12,629] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:12,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:12,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:12,647] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:12,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:12,647] [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	100.0	977	983	95	conclusive
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	77.4458	194	983	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.1486	54	983	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	76.8089	62	983	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	76.8089	62	983	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.8075	61	983	95	below_threshold
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	76.665	67	983	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	76.6592	66	983	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.6554	66	983	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.5695	74	983	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.5284	76	983	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	76.4746	68	983	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	76.4609	65	983	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	76.3644	70	983	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.3598	72	983	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	76.3485	64	983	95	below_threshold
Priestia aryabhattai	strain=B8W22	GCA_000956595.1	412384	412384	type	True	76.3382	61	983	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	76.2658	72	983	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	76.1502	71	983	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.1055	71	983	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	76.0247	71	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:12,649] [INFO] DFAST Taxonomy check result was written to GCF_009996845.1_ASM999684v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:12,650] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:12,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:12,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/checkm_data
[2024-01-24 13:02:12,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:12,690] [INFO] Task started: CheckM
[2024-01-24 13:02:12,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009996845.1_ASM999684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009996845.1_ASM999684v1_genomic.fna/checkm_input GCF_009996845.1_ASM999684v1_genomic.fna/checkm_result
[2024-01-24 13:02:37,727] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:37,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:37,752] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:37,752] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:37,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009996845.1_ASM999684v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:37,753] [INFO] Task started: Blastn
[2024-01-24 13:02:37,753] [INFO] Running command: blastn -query GCF_009996845.1_ASM999684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95e502da-5377-4f2f-bbc4-0f5daf44cff2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009996845.1_ASM999684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:38,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:38,658] [INFO] Selected 26 target genomes.
[2024-01-24 13:02:38,658] [INFO] Target genome list was writen to GCF_009996845.1_ASM999684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:38,678] [INFO] Task started: fastANI
[2024-01-24 13:02:38,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5ec182-4628-4eaf-a934-0e89b48f840d/GCF_009996845.1_ASM999684v1_genomic.fna.gz --refList GCF_009996845.1_ASM999684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009996845.1_ASM999684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:56,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:56,033] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:56,033] [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_009996845.1	s__RUG14133 sp009996845	100.0	977	983	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
GCA_902796085.1	s__RUG14133 sp902796085	81.9194	486	983	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	77.4647	195	983	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_003667825.1	s__Metabacillus litoralis_B	77.362	54	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_900156865.1	s__Fredinandcohnia sinesaloumensis	77.1013	58	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343615.1	s__Margalitia sp018343615	77.0236	55	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772965.1	s__Ureibacillus massiliensis	76.8089	62	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002844575.1	s__Margalitia camelliae	76.8075	61	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_000482325.1	s__Neobacillus sp000482325	76.804	55	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720625.1	s__Metabacillus sp004801455	76.6592	66	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006546985.1	s__VATK01 sp006546985	76.5668	60	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__VATK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013760845.1	s__Anoxybacillus_B calidus	76.521	66	983	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_012843265.1	s__Bacillus_BU sp012843265	76.5117	55	983	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_018332475.1	s__Bacillus_A sp018332475	76.3598	72	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.31	95.31	0.87	0.87	2	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	76.3485	64	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_900094905.1	s__Bacillus_A cereus_AG	76.2207	68	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.51	99.13	0.92	0.90	3	-
GCF_008923725.1	s__Bacillus_A sp008923725	76.2155	79	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007679095.1	s__DE0126 sp007679095	76.1363	79	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884185.1	s__Bacillus_A albus	76.0465	74	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.54	95.46	0.90	0.83	25	-
GCF_001883995.1	s__Bacillus_A paranthracis	76.0033	72	983	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_006494425.1	s__Bacillus_A sp006494425	75.9635	66	983	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,035] [INFO] GTDB search result was written to GCF_009996845.1_ASM999684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:56,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:56,042] [INFO] DFAST_QC result json was written to GCF_009996845.1_ASM999684v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:56,042] [INFO] DFAST_QC completed!
[2024-01-24 13:02:56,042] [INFO] Total running time: 0h1m17s