[2024-01-24 13:18:55,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference
[2024-01-24 13:18:56,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,649] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,649] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb5a23f6-0763-4860-83c0-3871cd892fe5/GCF_009674805.1_ASM967480v1_genomic.fna.gz | prodigal -d GCF_009674805.1_ASM967480v1_genomic.fna/cds.fna -a GCF_009674805.1_ASM967480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:05,861] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:05,862] [INFO] Task started: HMMsearch
[2024-01-24 13:19:05,862] [INFO] Running command: hmmsearch --tblout GCF_009674805.1_ASM967480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/reference_markers.hmm GCF_009674805.1_ASM967480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:06,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:06,167] [INFO] Found 6/6 markers.
[2024-01-24 13:19:06,202] [INFO] Query marker FASTA was written to GCF_009674805.1_ASM967480v1_genomic.fna/markers.fasta
[2024-01-24 13:19:06,202] [INFO] Task started: Blastn
[2024-01-24 13:19:06,203] [INFO] Running command: blastn -query GCF_009674805.1_ASM967480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/reference_markers.fasta -out GCF_009674805.1_ASM967480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:06,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:06,809] [INFO] Selected 27 target genomes.
[2024-01-24 13:19:06,809] [INFO] Target genome list was writen to GCF_009674805.1_ASM967480v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:06,824] [INFO] Task started: fastANI
[2024-01-24 13:19:06,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5a23f6-0763-4860-83c0-3871cd892fe5/GCF_009674805.1_ASM967480v1_genomic.fna.gz --refList GCF_009674805.1_ASM967480v1_genomic.fna/target_genomes.txt --output GCF_009674805.1_ASM967480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:23,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:23,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:23,273] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:23,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:23,273] [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
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	100.0	1307	1315	95	conclusive
Bacillus atrophaeus	strain=NBRC 15539	GCA_001591925.1	1452	1452	type	True	77.5634	75	1315	95	below_threshold
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	77.504	75	1315	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.4789	68	1315	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	77.3859	129	1315	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	77.3761	66	1315	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.3495	74	1315	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.2664	107	1315	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.1946	126	1315	95	below_threshold
Falsibacillus pallidus	strain=DSM 25281	GCA_003350505.1	493781	493781	type	True	77.1258	65	1315	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	77.1222	101	1315	95	below_threshold
Metabacillus kandeliae	strain=GX 13764	GCA_021166585.1	2900151	2900151	type	True	77.0536	122	1315	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.0363	59	1315	95	below_threshold
Peribacillus saganii	strain=V47-23a	GCA_003429095.1	2303992	2303992	type	True	76.9248	71	1315	95	below_threshold
Metabacillus mangrovi	strain=KCTC 33872	GCA_009711125.1	1491830	1491830	type	True	76.8504	116	1315	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	76.8314	68	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:23,275] [INFO] DFAST Taxonomy check result was written to GCF_009674805.1_ASM967480v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:23,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:23,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:23,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/checkm_data
[2024-01-24 13:19:23,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:23,317] [INFO] Task started: CheckM
[2024-01-24 13:19:23,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674805.1_ASM967480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674805.1_ASM967480v1_genomic.fna/checkm_input GCF_009674805.1_ASM967480v1_genomic.fna/checkm_result
[2024-01-24 13:19:57,892] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:57,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:57,909] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:57,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:57,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674805.1_ASM967480v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:57,911] [INFO] Task started: Blastn
[2024-01-24 13:19:57,911] [INFO] Running command: blastn -query GCF_009674805.1_ASM967480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28972182-c501-4624-a828-83cafa7ec5a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674805.1_ASM967480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:58,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:58,738] [INFO] Selected 26 target genomes.
[2024-01-24 13:19:58,739] [INFO] Target genome list was writen to GCF_009674805.1_ASM967480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:58,781] [INFO] Task started: fastANI
[2024-01-24 13:19:58,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5a23f6-0763-4860-83c0-3871cd892fe5/GCF_009674805.1_ASM967480v1_genomic.fna.gz --refList GCF_009674805.1_ASM967480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674805.1_ASM967480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:18,177] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:18,196] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:18,196] [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_009674805.1	s__Metabacillus_C lacus	100.0	1307	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000262045.1	s__Bacillus siamensis	77.6638	67	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.73	0.95	0.92	11	-
GCF_000473245.1	s__Bacillus_AB infantis	77.5008	91	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AB	95.0	98.14	95.38	0.91	0.87	7	-
GCF_001636425.1	s__Bacillus_AE acidicola	77.4633	66	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708755.2	s__Bacillus_P indicus	77.3641	130	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_000732485.2	s__Metabacillus_B sp000732485	77.3577	131	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003816055.1	s__Metabacillus_B sp003816055	77.2485	131	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274725.1	s__Cytobacillus globisporus	77.2248	88	1315	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_902829255.1	s__Metabacillus niabensis	77.2088	87	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_018283675.1	s__Metabacillus_B sp018283675	77.1985	126	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	77.1232	100	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303275.1	s__Cytobacillus sp017303275	77.0742	93	1315	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_001592005.1	s__Bacillus sonorensis	77.0716	77	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_003429095.1	s__Peribacillus_A saganii	76.9314	71	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773385.1	s__IB182487 sp014773385	76.909	110	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__IB182487	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636345.1	s__Cytobacillus gottheilii	76.8984	93	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_000981385.1	s__Metabacillus sp000981385	76.8604	96	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	76.8517	107	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711125.1	s__Metabacillus_B mangrovi	76.8504	116	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613035.1	s__Cytobacillus sp018613035	76.8273	96	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	76.8006	84	1315	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_900103525.1	s__Neobacillus sp900103525	76.7671	60	1315	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_014235785.1	s__Bacillus_P sp002858905	76.6558	105	1315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.85	98.20	0.93	0.90	4	-
GCF_000712595.1	s__Bacillus_A manliponensis	76.5205	55	1315	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 13:20:18,198] [INFO] GTDB search result was written to GCF_009674805.1_ASM967480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:18,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:18,203] [INFO] DFAST_QC result json was written to GCF_009674805.1_ASM967480v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:18,203] [INFO] DFAST_QC completed!
[2024-01-24 13:20:18,203] [INFO] Total running time: 0h1m23s