[2024-01-25 19:05:35,580] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:35,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:35,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference
[2024-01-25 19:05:36,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:36,772] [INFO] Task started: Prodigal
[2024-01-25 19:05:36,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d054391-77e7-44ef-94ad-7cad2afe78a3/GCF_014638355.1_ASM1463835v1_genomic.fna.gz | prodigal -d GCF_014638355.1_ASM1463835v1_genomic.fna/cds.fna -a GCF_014638355.1_ASM1463835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:43,923] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:43,924] [INFO] Task started: HMMsearch
[2024-01-25 19:05:43,924] [INFO] Running command: hmmsearch --tblout GCF_014638355.1_ASM1463835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/reference_markers.hmm GCF_014638355.1_ASM1463835v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:44,189] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:44,190] [INFO] Found 6/6 markers.
[2024-01-25 19:05:44,218] [INFO] Query marker FASTA was written to GCF_014638355.1_ASM1463835v1_genomic.fna/markers.fasta
[2024-01-25 19:05:44,218] [INFO] Task started: Blastn
[2024-01-25 19:05:44,218] [INFO] Running command: blastn -query GCF_014638355.1_ASM1463835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/reference_markers.fasta -out GCF_014638355.1_ASM1463835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:44,796] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:44,800] [INFO] Selected 31 target genomes.
[2024-01-25 19:05:44,800] [INFO] Target genome list was writen to GCF_014638355.1_ASM1463835v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:44,816] [INFO] Task started: fastANI
[2024-01-25 19:05:44,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d054391-77e7-44ef-94ad-7cad2afe78a3/GCF_014638355.1_ASM1463835v1_genomic.fna.gz --refList GCF_014638355.1_ASM1463835v1_genomic.fna/target_genomes.txt --output GCF_014638355.1_ASM1463835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:04,798] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:04,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:04,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:04,810] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:06:04,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:04,810] [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
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	100.0	1264	1264	95	conclusive
Priestia taiwanensis	strain=DSM 27845	GCA_016908755.1	1347902	1347902	type	True	99.9953	1262	1264	95	conclusive
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	77.5891	161	1264	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	77.5729	216	1264	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_000161615.1	1428	1428	suspected-type	True	77.5484	212	1264	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	77.4664	218	1264	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	77.414	217	1264	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	77.3652	229	1264	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.3428	219	1264	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	77.2597	200	1264	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	77.2235	92	1264	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	77.0279	91	1264	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.693	64	1264	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	76.6126	50	1264	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.5737	73	1264	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.5611	76	1264	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.5364	78	1264	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.373	84	1264	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.3086	67	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:04,813] [INFO] DFAST Taxonomy check result was written to GCF_014638355.1_ASM1463835v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:04,814] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:04,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:04,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/checkm_data
[2024-01-25 19:06:04,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:04,855] [INFO] Task started: CheckM
[2024-01-25 19:06:04,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638355.1_ASM1463835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638355.1_ASM1463835v1_genomic.fna/checkm_input GCF_014638355.1_ASM1463835v1_genomic.fna/checkm_result
[2024-01-25 19:06:30,538] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:30,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:30,557] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:30,557] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:30,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638355.1_ASM1463835v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:30,557] [INFO] Task started: Blastn
[2024-01-25 19:06:30,557] [INFO] Running command: blastn -query GCF_014638355.1_ASM1463835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6314063-f11b-493f-96b2-322903e14b67/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638355.1_ASM1463835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:31,362] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:31,365] [INFO] Selected 36 target genomes.
[2024-01-25 19:06:31,365] [INFO] Target genome list was writen to GCF_014638355.1_ASM1463835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:31,406] [INFO] Task started: fastANI
[2024-01-25 19:06:31,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d054391-77e7-44ef-94ad-7cad2afe78a3/GCF_014638355.1_ASM1463835v1_genomic.fna.gz --refList GCF_014638355.1_ASM1463835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638355.1_ASM1463835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:58,352] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:58,367] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:58,367] [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_014638355.1	s__Priestia_D taiwanensis	100.0	1264	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Priestia_D	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002574955.1	s__Bacillus_A cereus_AT	77.6403	206	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	99.26	96.80	0.94	0.81	6	-
GCF_002571225.1	s__Bacillus_A sp002571225	77.6238	204	1264	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	77.5959	212	1264	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_000017425.1	s__Bacillus_A cytotoxicus	77.5891	161	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.49	99.12	0.95	0.93	21	-
GCF_000021305.1	s__Bacillus_A thuringiensis_S	77.5739	208	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.4134	98.69	97.04	0.88	0.75	230	-
GCF_900116295.1	s__Bacillus_A sp900116295	77.5305	203	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	77.5172	207	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_002746455.1	s__Bacillus_A fungorum	77.5098	207	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.51	97.51	0.90	0.90	2	-
GCF_014932895.1	s__Bacillus_A thuringiensis_AA	77.4996	202	1264	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_001884065.1	s__Bacillus_A proteolyticus	77.4806	217	1264	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_000299035.1	s__Bacillus_A bingmayongensis	77.4705	192	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_002561295.1	s__Bacillus_A cereus_S	77.4615	196	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
GCF_001884135.1	s__Bacillus_A nitratireducens	77.4278	217	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.14	95.62	0.90	0.85	78	-
GCF_000380245.2	s__Bacillus_AD massiliogorillae	77.2285	91	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.1864	103	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.0947	79	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799755.1	s__Fredinandcohnia timonensis_A	76.9976	70	1264	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_001591565.1	s__Priestia flexa	76.8708	85	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
GCF_003184905.1	s__Priestia sp003184905	76.7986	116	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902374955.1	s__Bacillus_AD massilioanorexius	76.7849	73	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003586445.1	s__Robertmurraya sp003586445	76.7362	72	1264	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_003073175.1	s__Bacillus_BN acanthi	76.693	64	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104555.1	s__Litchfieldia salsa	76.566	72	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001938995.1	s__Bacillus pumilus_G	76.4146	53	1264	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	76.4098	75	1264	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_002835805.1	s__Niallia nealsonii	76.3086	67	1264	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:58,369] [INFO] GTDB search result was written to GCF_014638355.1_ASM1463835v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:58,370] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:58,374] [INFO] DFAST_QC result json was written to GCF_014638355.1_ASM1463835v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:58,375] [INFO] DFAST_QC completed!
[2024-01-25 19:06:58,375] [INFO] Total running time: 0h1m23s