[2024-01-25 17:35:50,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:50,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:50,704] [INFO] DQC Reference Directory: /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference
[2024-01-25 17:35:51,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:51,789] [INFO] Task started: Prodigal
[2024-01-25 17:35:51,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgb57a9959-3fd6-4370-9898-c93e01627738/GCF_014773385.1_ASM1477338v1_genomic.fna.gz | prodigal -d GCF_014773385.1_ASM1477338v1_genomic.fna/cds.fna -a GCF_014773385.1_ASM1477338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:01,537] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:01,538] [INFO] Task started: HMMsearch
[2024-01-25 17:36:01,538] [INFO] Running command: hmmsearch --tblout GCF_014773385.1_ASM1477338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/reference_markers.hmm GCF_014773385.1_ASM1477338v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:01,798] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:01,800] [INFO] Found 6/6 markers.
[2024-01-25 17:36:01,842] [INFO] Query marker FASTA was written to GCF_014773385.1_ASM1477338v1_genomic.fna/markers.fasta
[2024-01-25 17:36:01,842] [INFO] Task started: Blastn
[2024-01-25 17:36:01,842] [INFO] Running command: blastn -query GCF_014773385.1_ASM1477338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/reference_markers.fasta -out GCF_014773385.1_ASM1477338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:02,403] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:02,405] [INFO] Selected 29 target genomes.
[2024-01-25 17:36:02,406] [INFO] Target genome list was writen to GCF_014773385.1_ASM1477338v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:02,429] [INFO] Task started: fastANI
[2024-01-25 17:36:02,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57a9959-3fd6-4370-9898-c93e01627738/GCF_014773385.1_ASM1477338v1_genomic.fna.gz --refList GCF_014773385.1_ASM1477338v1_genomic.fna/target_genomes.txt --output GCF_014773385.1_ASM1477338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:24,888] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:24,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:24,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:24,904] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:24,904] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:24,904] [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 bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	78.5539	275	1838	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	78.2963	247	1838	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	78.2418	251	1838	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.9662	216	1838	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.4032	190	1838	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	77.3621	186	1838	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	77.102	173	1838	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.9702	93	1838	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	76.9451	84	1838	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.8997	111	1838	95	below_threshold
Bacillus marasmi	strain=Marseille-P3556	GCA_902168435.1	1926279	1926279	type	True	76.6314	89	1838	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	76.6275	111	1838	95	below_threshold
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	76.5785	112	1838	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.5671	95	1838	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.5445	114	1838	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.4927	83	1838	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.4493	92	1838	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	76.4469	114	1838	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.4309	74	1838	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.4029	92	1838	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	76.3641	71	1838	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.3598	111	1838	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.3467	77	1838	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:24,906] [INFO] DFAST Taxonomy check result was written to GCF_014773385.1_ASM1477338v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:24,906] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:24,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:24,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/checkm_data
[2024-01-25 17:36:24,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:24,961] [INFO] Task started: CheckM
[2024-01-25 17:36:24,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773385.1_ASM1477338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773385.1_ASM1477338v1_genomic.fna/checkm_input GCF_014773385.1_ASM1477338v1_genomic.fna/checkm_result
[2024-01-25 17:36:57,243] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:57,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:57,263] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:57,263] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:57,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773385.1_ASM1477338v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:57,264] [INFO] Task started: Blastn
[2024-01-25 17:36:57,264] [INFO] Running command: blastn -query GCF_014773385.1_ASM1477338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8062b84-a10f-4dbd-b82c-c55bd7f4b511/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773385.1_ASM1477338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:58,124] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:58,127] [INFO] Selected 26 target genomes.
[2024-01-25 17:36:58,127] [INFO] Target genome list was writen to GCF_014773385.1_ASM1477338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:58,139] [INFO] Task started: fastANI
[2024-01-25 17:36:58,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgb57a9959-3fd6-4370-9898-c93e01627738/GCF_014773385.1_ASM1477338v1_genomic.fna.gz --refList GCF_014773385.1_ASM1477338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773385.1_ASM1477338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:18,676] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:18,689] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:18,689] [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_014773385.1	s__IB182487 sp014773385	100.0	1835	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__IB182487	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014217835.1	s__Metabacillus litoralis_A	78.7311	252	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_017497975.1	s__Metabacillus sp017497975	78.5541	275	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235785.1	s__Bacillus_P sp002858905	77.5022	154	1838	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_014960805.1	s__Bacillus_BV sp014960805	77.4797	72	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518865.1	s__Metabacillus sp000518865	77.0313	176	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	76.9026	166	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636345.1	s__Cytobacillus gottheilii	76.8941	86	1838	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_902168435.1	s__Bacillus_BU marasmi	76.7053	88	1838	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_900166665.1	s__Cytobacillus gottheilii_A	76.676	87	1838	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_013761245.1	s__Anoxybacillus_C caldiproteolyticus	76.6725	64	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_C	95.0	99.29	99.25	0.94	0.93	3	-
GCF_004358205.1	s__Neobacillus salipaludis	76.6661	111	1838	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_002744245.1	s__Bacillus pumilus_M	76.5953	88	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001938995.1	s__Bacillus pumilus_G	76.5907	84	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674805.1	s__Metabacillus_C lacus	76.5785	112	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250055.1	s__Sutcliffiella cohnii	76.566	113	1838	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_000712595.1	s__Bacillus_A manliponensis	76.5309	85	1838	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_016908395.1	s__Metabacillus crassostreae	76.5216	167	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938125.1	s__Rossellomorea sp005938125	76.4857	63	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156875.1	s__Robertmurraya dakarensis	76.4469	114	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836495.1	s__Cytobacillus sp014836495	76.3729	76	1838	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_003667865.1	s__Bacillus_BQ marisflavi_A	76.2429	74	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591565.1	s__Priestia flexa	76.1992	97	1838	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:18,691] [INFO] GTDB search result was written to GCF_014773385.1_ASM1477338v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:18,692] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:18,700] [INFO] DFAST_QC result json was written to GCF_014773385.1_ASM1477338v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:18,700] [INFO] DFAST_QC completed!
[2024-01-25 17:37:18,700] [INFO] Total running time: 0h1m28s