[2024-01-24 14:28:07,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:07,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:07,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference
[2024-01-24 14:28:10,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,427] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,427] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4a6d329-b877-40a6-abfd-22365ba98694/GCF_014207535.1_ASM1420753v1_genomic.fna.gz | prodigal -d GCF_014207535.1_ASM1420753v1_genomic.fna/cds.fna -a GCF_014207535.1_ASM1420753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:21,536] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:21,536] [INFO] Task started: HMMsearch
[2024-01-24 14:28:21,536] [INFO] Running command: hmmsearch --tblout GCF_014207535.1_ASM1420753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/reference_markers.hmm GCF_014207535.1_ASM1420753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:21,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:21,867] [INFO] Found 6/6 markers.
[2024-01-24 14:28:21,909] [INFO] Query marker FASTA was written to GCF_014207535.1_ASM1420753v1_genomic.fna/markers.fasta
[2024-01-24 14:28:21,910] [INFO] Task started: Blastn
[2024-01-24 14:28:21,910] [INFO] Running command: blastn -query GCF_014207535.1_ASM1420753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/reference_markers.fasta -out GCF_014207535.1_ASM1420753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:22,603] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:22,607] [INFO] Selected 29 target genomes.
[2024-01-24 14:28:22,607] [INFO] Target genome list was writen to GCF_014207535.1_ASM1420753v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:22,621] [INFO] Task started: fastANI
[2024-01-24 14:28:22,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a6d329-b877-40a6-abfd-22365ba98694/GCF_014207535.1_ASM1420753v1_genomic.fna.gz --refList GCF_014207535.1_ASM1420753v1_genomic.fna/target_genomes.txt --output GCF_014207535.1_ASM1420753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:46,001] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:46,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:46,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:46,023] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:46,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:46,023] [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
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	100.0	1533	1539	95	conclusive
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.8065	155	1539	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.7198	125	1539	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.6824	118	1539	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.6824	118	1539	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	77.6667	118	1539	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.5973	135	1539	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.5461	140	1539	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.4994	141	1539	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.4058	133	1539	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.3818	149	1539	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	77.2847	133	1539	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.2121	70	1539	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.1749	138	1539	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	77.1545	108	1539	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	77.1239	116	1539	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.1002	59	1539	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.0825	148	1539	95	below_threshold
Neobacillus bataviensis	strain=LMG 21833	GCA_000307875.1	220685	220685	type	True	77.0503	131	1539	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.0186	116	1539	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.9728	139	1539	95	below_threshold
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	76.9567	79	1539	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.8938	79	1539	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	76.6275	50	1539	95	below_threshold
Priestia filamentosa	strain=SGD-14	GCA_900177535.1	1402861	1402861	type	True	76.3815	65	1539	95	below_threshold
Priestia filamentosa	strain=DSM 27955	GCA_002237735.1	1402861	1402861	type	True	76.3409	64	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:46,025] [INFO] DFAST Taxonomy check result was written to GCF_014207535.1_ASM1420753v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:46,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:46,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:46,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/checkm_data
[2024-01-24 14:28:46,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:46,076] [INFO] Task started: CheckM
[2024-01-24 14:28:46,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207535.1_ASM1420753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207535.1_ASM1420753v1_genomic.fna/checkm_input GCF_014207535.1_ASM1420753v1_genomic.fna/checkm_result
[2024-01-24 14:29:22,844] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:22,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:22,863] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:22,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:22,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207535.1_ASM1420753v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:22,865] [INFO] Task started: Blastn
[2024-01-24 14:29:22,865] [INFO] Running command: blastn -query GCF_014207535.1_ASM1420753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg838eaadf-fdf2-41f2-b27c-aa0d203198cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207535.1_ASM1420753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:23,693] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:23,698] [INFO] Selected 25 target genomes.
[2024-01-24 14:29:23,698] [INFO] Target genome list was writen to GCF_014207535.1_ASM1420753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:23,740] [INFO] Task started: fastANI
[2024-01-24 14:29:23,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a6d329-b877-40a6-abfd-22365ba98694/GCF_014207535.1_ASM1420753v1_genomic.fna.gz --refList GCF_014207535.1_ASM1420753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207535.1_ASM1420753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:44,697] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:44,717] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:44,717] [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_014207535.1	s__Bacillus_BD benzoevorans	100.0	1533	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008710145.1	s__Bacillus_BD endozanthoxylicus	78.5958	339	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104575.1	s__Bacillus_BD tuaregi	78.1555	285	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686805.1	s__Neobacillus sp000686805	78.0559	149	1539	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_011250555.1	s__Neobacillus sp011250555	77.7209	126	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001636345.1	s__Cytobacillus gottheilii	77.6719	123	1539	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_017355915.1	s__Mesobacillus sp017355915	77.5999	90	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	77.5239	141	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_014138605.1	s__Peribacillus huizhouensis	77.4959	101	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	98.72	98.72	0.94	0.94	2	-
GCF_006546985.1	s__VATK01 sp006546985	77.4543	117	1539	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_000242895.2	s__Bacillus_BU sp000242895	77.4462	144	1539	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_900199725.1	s__Cytobacillus massiliigabonensis	77.4437	143	1539	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_002860255.1	s__Neobacillus cucumis_A	77.4397	136	1539	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_014656545.1	s__Neobacillus sp014656545	77.4283	132	1539	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_003182355.1	s__Cytobacillus oceanisediminis_A	77.3421	128	1539	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_001591805.1	s__Neobacillus novalis	77.2847	133	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017303275.1	s__Cytobacillus sp017303275	77.27	138	1539	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_004366035.1	s__Cytobacillus oceanisediminis_C	77.2215	126	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002835805.1	s__Niallia nealsonii	77.154	107	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612625.1	s__Neobacillus jeddahensis	77.0723	116	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000307875.1	s__Neobacillus bataviensis	77.0503	131	1539	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_016464375.1	s__Neobacillus renqingensis	76.5941	114	1539	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_900177535.1	s__Bacillus_I filamentosa	76.3408	64	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	99.55	98.90	0.95	0.92	6	-
GCF_001712755.1	s__Gottfriedia luciferensis_B	76.183	53	1539	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:44,719] [INFO] GTDB search result was written to GCF_014207535.1_ASM1420753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:44,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:44,728] [INFO] DFAST_QC result json was written to GCF_014207535.1_ASM1420753v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:44,728] [INFO] DFAST_QC completed!
[2024-01-24 14:29:44,728] [INFO] Total running time: 0h1m37s