[2024-01-24 11:44:05,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference
[2024-01-24 11:44:08,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,843] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg35a43b48-8f26-4fa4-9e97-597d55f2fa38/GCF_016772275.1_ASM1677227v1_genomic.fna.gz | prodigal -d GCF_016772275.1_ASM1677227v1_genomic.fna/cds.fna -a GCF_016772275.1_ASM1677227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:17,649] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:17,650] [INFO] Task started: HMMsearch
[2024-01-24 11:44:17,650] [INFO] Running command: hmmsearch --tblout GCF_016772275.1_ASM1677227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/reference_markers.hmm GCF_016772275.1_ASM1677227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:17,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:17,960] [INFO] Found 6/6 markers.
[2024-01-24 11:44:17,999] [INFO] Query marker FASTA was written to GCF_016772275.1_ASM1677227v1_genomic.fna/markers.fasta
[2024-01-24 11:44:18,000] [INFO] Task started: Blastn
[2024-01-24 11:44:18,000] [INFO] Running command: blastn -query GCF_016772275.1_ASM1677227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/reference_markers.fasta -out GCF_016772275.1_ASM1677227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:18,612] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:18,616] [INFO] Selected 27 target genomes.
[2024-01-24 11:44:18,616] [INFO] Target genome list was writen to GCF_016772275.1_ASM1677227v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:18,730] [INFO] Task started: fastANI
[2024-01-24 11:44:18,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg35a43b48-8f26-4fa4-9e97-597d55f2fa38/GCF_016772275.1_ASM1677227v1_genomic.fna.gz --refList GCF_016772275.1_ASM1677227v1_genomic.fna/target_genomes.txt --output GCF_016772275.1_ASM1677227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:40,414] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:40,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:40,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:40,438] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:40,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:40,439] [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
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	100.0	1436	1436	95	conclusive
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	89.5167	839	1436	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	89.4363	924	1436	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	79.7813	525	1436	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	79.756	523	1436	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.3371	130	1436	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	79.1864	302	1436	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.1564	93	1436	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	78.8617	87	1436	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	78.7865	141	1436	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	78.3395	288	1436	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.8554	114	1436	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.3901	99	1436	95	below_threshold
Weizmannia ginsengihumi	strain=Gsoil 114	GCA_011008565.1	363870	363870	type	True	77.3237	159	1436	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.0947	127	1436	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.083	105	1436	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.0456	108	1436	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.7648	114	1436	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	76.7315	65	1436	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6637	119	1436	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.641	94	1436	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.5508	114	1436	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	76.4302	81	1436	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.3531	73	1436	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.1597	61	1436	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	75.9786	79	1436	95	below_threshold
Bacillus luti	strain=TD41	GCA_001884105.1	2026191	2026191	type	True	75.8108	88	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:40,440] [INFO] DFAST Taxonomy check result was written to GCF_016772275.1_ASM1677227v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:40,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:40,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:40,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/checkm_data
[2024-01-24 11:44:40,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:40,484] [INFO] Task started: CheckM
[2024-01-24 11:44:40,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016772275.1_ASM1677227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016772275.1_ASM1677227v1_genomic.fna/checkm_input GCF_016772275.1_ASM1677227v1_genomic.fna/checkm_result
[2024-01-24 11:45:11,829] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:11,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:11,849] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:11,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:11,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016772275.1_ASM1677227v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:11,850] [INFO] Task started: Blastn
[2024-01-24 11:45:11,850] [INFO] Running command: blastn -query GCF_016772275.1_ASM1677227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58b99e3-25e2-4abf-b618-81aac2dc8418/dqc_reference/reference_markers_gtdb.fasta -out GCF_016772275.1_ASM1677227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:12,667] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:12,671] [INFO] Selected 25 target genomes.
[2024-01-24 11:45:12,672] [INFO] Target genome list was writen to GCF_016772275.1_ASM1677227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:12,689] [INFO] Task started: fastANI
[2024-01-24 11:45:12,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg35a43b48-8f26-4fa4-9e97-597d55f2fa38/GCF_016772275.1_ASM1677227v1_genomic.fna.gz --refList GCF_016772275.1_ASM1677227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016772275.1_ASM1677227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:37,049] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:37,074] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:37,075] [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_016772275.1	s__Heyndrickxia vini	100.0	1436	1436	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	conclusive
GCF_016756695.1	s__Heyndrickxia sporothermodurans	89.2524	1025	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_003600835.1	s__Pseudobacillus sp003600835	79.7977	104	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017809215.1	s__Heyndrickxia oleronia	79.7813	522	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_001636315.1	s__Neobacillus mesonae	79.3507	128	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	79.25	573	1436	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_001420715.1	s__Margalitia shackletonii	79.0953	301	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_018343615.1	s__Margalitia sp018343615	78.5388	266	1436	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_001048695.1	s__Neobacillus massiliamazoniensis	77.8128	118	1436	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_000518865.1	s__Metabacillus sp000518865	77.7355	119	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975035.1	s__Neobacillus thermocopriae	77.3626	100	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_011008565.1	s__Weizmannia ginsengihum	77.2561	163	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.62	99.53	0.95	0.92	4	-
GCF_000307875.1	s__Neobacillus bataviensis	77.1254	121	1436	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_017497975.1	s__Metabacillus sp017497975	77.1041	124	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591505.1	s__Neobacillus niacini	77.012	115	1436	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_003966145.1	s__Ureibacillus telephonicus	76.8891	84	1436	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_900220965.1	s__Ureibacillus acetophenoni	76.7314	65	1436	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_014932895.1	s__Bacillus_A thuringiensis_AA	76.4217	86	1436	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_008923725.1	s__Bacillus_A sp008923725	76.4159	87	1436	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_002564555.1	s__Bacillus_A cereus_K	76.3694	68	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.77	97.26	0.94	0.89	7	-
GCF_000392615.1	s__Lysinibacillus sphaericus_B	76.2771	53	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002578045.1	s__Bacillus_A cereus_AK	76.2699	88	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.93	99.93	0.97	0.97	2	-
GCF_001884065.1	s__Bacillus_A proteolyticus	76.1026	73	1436	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	98.61	98.37	0.91	0.91	4	-
GCF_001883995.1	s__Bacillus_A paranthracis	75.9583	80	1436	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_001884185.1	s__Bacillus_A albus	75.7934	94	1436	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:37,087] [INFO] GTDB search result was written to GCF_016772275.1_ASM1677227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:37,088] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:37,095] [INFO] DFAST_QC result json was written to GCF_016772275.1_ASM1677227v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:37,095] [INFO] DFAST_QC completed!
[2024-01-24 11:45:37,095] [INFO] Total running time: 0h1m32s