[2024-01-25 17:53:06,028] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:06,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:06,030] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference
[2024-01-25 17:53:07,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:07,142] [INFO] Task started: Prodigal
[2024-01-25 17:53:07,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b5b5185-ffc3-4f2a-b500-7708d22edc13/GCF_022808645.1_ASM2280864v1_genomic.fna.gz | prodigal -d GCF_022808645.1_ASM2280864v1_genomic.fna/cds.fna -a GCF_022808645.1_ASM2280864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:14,930] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:14,931] [INFO] Task started: HMMsearch
[2024-01-25 17:53:14,931] [INFO] Running command: hmmsearch --tblout GCF_022808645.1_ASM2280864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/reference_markers.hmm GCF_022808645.1_ASM2280864v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:15,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:15,209] [INFO] Found 6/6 markers.
[2024-01-25 17:53:15,252] [INFO] Query marker FASTA was written to GCF_022808645.1_ASM2280864v1_genomic.fna/markers.fasta
[2024-01-25 17:53:15,253] [INFO] Task started: Blastn
[2024-01-25 17:53:15,253] [INFO] Running command: blastn -query GCF_022808645.1_ASM2280864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/reference_markers.fasta -out GCF_022808645.1_ASM2280864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:15,825] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:15,827] [INFO] Selected 30 target genomes.
[2024-01-25 17:53:15,828] [INFO] Target genome list was writen to GCF_022808645.1_ASM2280864v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:15,840] [INFO] Task started: fastANI
[2024-01-25 17:53:15,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5b5185-ffc3-4f2a-b500-7708d22edc13/GCF_022808645.1_ASM2280864v1_genomic.fna.gz --refList GCF_022808645.1_ASM2280864v1_genomic.fna/target_genomes.txt --output GCF_022808645.1_ASM2280864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:36,709] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:36,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:36,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:36,724] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:53:36,725] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:53:36,725] [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 oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	84.2574	1086	1426	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	77.4732	85	1426	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	77.3083	81	1426	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.0969	80	1426	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.9395	100	1426	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.8572	70	1426	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	76.7775	52	1426	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.7439	71	1426	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.7156	54	1426	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	76.7006	80	1426	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.6756	55	1426	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	76.6588	84	1426	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.6509	79	1426	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	76.637	50	1426	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	76.6091	50	1426	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	76.6038	50	1426	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.5543	103	1426	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.542	84	1426	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	76.5363	90	1426	95	below_threshold
Niallia taxi	strain=M5HDSG1-1	GCA_004005475.1	2499688	2499688	type	True	76.4428	67	1426	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	76.39	92	1426	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	76.3141	84	1426	95	below_threshold
Anoxybacillus rupiensis	strain=DSM 17127	GCA_014196195.1	311460	311460	type	True	76.3089	57	1426	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	76.2443	71	1426	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.2428	68	1426	95	below_threshold
Calidifontibacillus oryziterrae	strain=ZYK	GCA_000331575.1	1191699	1191699	type	True	75.9356	51	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:36,726] [INFO] DFAST Taxonomy check result was written to GCF_022808645.1_ASM2280864v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:36,727] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:36,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:36,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/checkm_data
[2024-01-25 17:53:36,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:36,772] [INFO] Task started: CheckM
[2024-01-25 17:53:36,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022808645.1_ASM2280864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022808645.1_ASM2280864v1_genomic.fna/checkm_input GCF_022808645.1_ASM2280864v1_genomic.fna/checkm_result
[2024-01-25 17:54:04,604] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:04,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:04,622] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:04,622] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:04,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022808645.1_ASM2280864v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:04,623] [INFO] Task started: Blastn
[2024-01-25 17:54:04,623] [INFO] Running command: blastn -query GCF_022808645.1_ASM2280864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc97f73b-ac7b-4d79-aa34-8d733320b958/dqc_reference/reference_markers_gtdb.fasta -out GCF_022808645.1_ASM2280864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:05,378] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:05,381] [INFO] Selected 29 target genomes.
[2024-01-25 17:54:05,381] [INFO] Target genome list was writen to GCF_022808645.1_ASM2280864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:05,397] [INFO] Task started: fastANI
[2024-01-25 17:54:05,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5b5185-ffc3-4f2a-b500-7708d22edc13/GCF_022808645.1_ASM2280864v1_genomic.fna.gz --refList GCF_022808645.1_ASM2280864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022808645.1_ASM2280864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:28,871] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:28,884] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:54:28,885] [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_900207585.1	s__Bacillus_BF oleivorans	84.2627	1085	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__JC228;f__JC228;g__Bacillus_BF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001076885.1	s__Niallia sp001076885	77.6714	75	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.59	99.45	0.92	0.91	4	-
GCF_005116465.1	s__Robertmurraya kyonggiensis	77.4927	104	1426	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_001420715.1	s__Margalitia shackletonii	77.4313	84	1426	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_000242895.2	s__Bacillus_BU sp000242895	77.1294	71	1426	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_900104555.1	s__Litchfieldia salsa	77.0969	80	1426	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_006546985.1	s__VATK01 sp006546985	77.0566	72	1426	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_016908495.1	s__Bacillus_BW pakistanensis	76.9629	99	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BW	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115925.1	s__CL95 sp900115925	76.8743	70	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__CL95	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002019645.1	s__Litchfieldia alkalitelluris	76.7425	69	1426	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_008923245.1	s__Cytobacillus depressus	76.6588	84	1426	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_002844575.1	s__Margalitia camelliae	76.6509	79	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_003688615.2	s__Parageobacillus toebii	76.637	50	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_004341175.1	s__Neobacillus sp004341175	76.5723	80	1426	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_001439605.1	s__Cytobacillus praedii	76.5543	103	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_018613035.1	s__Cytobacillus sp018613035	76.5404	93	1426	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_001026695.1	s__Neobacillus vireti	76.5363	90	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.4636	102	1426	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_000426085.1	s__URHB0009 sp000426085	76.4633	74	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008845.1	s__Bacillus_BS mesophilus	76.4193	54	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004005475.1	s__Niallia taxi	76.4122	68	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	97.90	96.11	0.92	0.86	5	-
GCF_002559665.1	s__Bacillus_A cereus_AV	76.3314	53	1426	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_001940785.1	s__Neobacillus sp001940785	76.2788	76	1426	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_001712755.1	s__Gottfriedia luciferensis_B	75.9983	62	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:28,887] [INFO] GTDB search result was written to GCF_022808645.1_ASM2280864v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:28,888] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:28,891] [INFO] DFAST_QC result json was written to GCF_022808645.1_ASM2280864v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:28,892] [INFO] DFAST_QC completed!
[2024-01-25 17:54:28,892] [INFO] Total running time: 0h1m23s