[2024-01-25 17:36:35,795] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:35,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:35,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference
[2024-01-25 17:36:36,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:36,943] [INFO] Task started: Prodigal
[2024-01-25 17:36:36,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c5d6322-b2c4-4a4f-9783-a187d3faf565/GCF_009466385.1_ASM946638v1_genomic.fna.gz | prodigal -d GCF_009466385.1_ASM946638v1_genomic.fna/cds.fna -a GCF_009466385.1_ASM946638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:43,030] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:43,030] [INFO] Task started: HMMsearch
[2024-01-25 17:36:43,030] [INFO] Running command: hmmsearch --tblout GCF_009466385.1_ASM946638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/reference_markers.hmm GCF_009466385.1_ASM946638v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:43,274] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:43,275] [INFO] Found 6/6 markers.
[2024-01-25 17:36:43,301] [INFO] Query marker FASTA was written to GCF_009466385.1_ASM946638v1_genomic.fna/markers.fasta
[2024-01-25 17:36:43,302] [INFO] Task started: Blastn
[2024-01-25 17:36:43,302] [INFO] Running command: blastn -query GCF_009466385.1_ASM946638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/reference_markers.fasta -out GCF_009466385.1_ASM946638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:43,912] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:43,915] [INFO] Selected 27 target genomes.
[2024-01-25 17:36:43,915] [INFO] Target genome list was writen to GCF_009466385.1_ASM946638v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:43,940] [INFO] Task started: fastANI
[2024-01-25 17:36:43,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d6322-b2c4-4a4f-9783-a187d3faf565/GCF_009466385.1_ASM946638v1_genomic.fna.gz --refList GCF_009466385.1_ASM946638v1_genomic.fna/target_genomes.txt --output GCF_009466385.1_ASM946638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:03,413] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:03,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:03,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:03,427] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:03,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:03,428] [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 tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	100.0	1088	1091	95	conclusive
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	78.1451	212	1091	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.9697	78	1091	95	below_threshold
Falsibacillus pallidus	strain=DSM 25281	GCA_003350505.1	493781	493781	type	True	77.7862	63	1091	95	below_threshold
Peribacillus saganii	strain=V47-23a	GCA_003429095.1	2303992	2303992	type	True	77.6915	112	1091	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.6162	111	1091	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	77.412	96	1091	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	77.4006	93	1091	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.3564	121	1091	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.3232	80	1091	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.3174	96	1091	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	77.2849	88	1091	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.2299	86	1091	95	below_threshold
Peribacillus cavernae	strain=L5	GCA_003989135.1	1674310	1674310	type	True	77.2257	110	1091	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	77.1697	91	1091	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.0641	109	1091	95	below_threshold
Jeotgalibacillus soli	strain=P9	GCA_000829435.1	889306	889306	type	True	77.0507	57	1091	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	76.9544	62	1091	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	76.9505	64	1091	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.9214	61	1091	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	76.7889	85	1091	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	76.627	94	1091	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	76.3041	62	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:03,429] [INFO] DFAST Taxonomy check result was written to GCF_009466385.1_ASM946638v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:03,429] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:03,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:03,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/checkm_data
[2024-01-25 17:37:03,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:03,465] [INFO] Task started: CheckM
[2024-01-25 17:37:03,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009466385.1_ASM946638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009466385.1_ASM946638v1_genomic.fna/checkm_input GCF_009466385.1_ASM946638v1_genomic.fna/checkm_result
[2024-01-25 17:37:27,276] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:27,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:27,297] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:27,297] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:27,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009466385.1_ASM946638v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:27,298] [INFO] Task started: Blastn
[2024-01-25 17:37:27,298] [INFO] Running command: blastn -query GCF_009466385.1_ASM946638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e175b71-774f-4c11-8c2d-2768464a5902/dqc_reference/reference_markers_gtdb.fasta -out GCF_009466385.1_ASM946638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:28,340] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:28,344] [INFO] Selected 28 target genomes.
[2024-01-25 17:37:28,344] [INFO] Target genome list was writen to GCF_009466385.1_ASM946638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:28,358] [INFO] Task started: fastANI
[2024-01-25 17:37:28,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d6322-b2c4-4a4f-9783-a187d3faf565/GCF_009466385.1_ASM946638v1_genomic.fna.gz --refList GCF_009466385.1_ASM946638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009466385.1_ASM946638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:49,702] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:49,718] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:49,718] [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_009466385.1	s__Bacillus_BN tepidiphilus	100.0	1088	1091	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	conclusive
GCA_017656295.1	s__JACDOC01 sp017656295	78.2047	109	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.7772	155	1091	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_003429095.1	s__Peribacillus_A saganii	77.7759	109	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350505.1	s__Falsibacillus pallidus	77.7119	62	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343715.1	s__FJAT-49711 sp018343715	77.6484	55	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909175.1	s__Bacillus_AI deserti	77.5879	110	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235785.1	s__Bacillus_P sp002858905	77.5871	65	1091	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_902374955.1	s__Bacillus_AD massilioanorexius	77.5213	133	1091	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_003600835.1	s__Pseudobacillus sp003600835	77.4952	72	1091	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_019039215.1	s__Cytobacillus sp019039215	77.3991	110	1091	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_000305495.1	s__Peribacillus psychrosaccharolyticus	77.3232	80	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_013248975.1	s__Neobacillus endophyticus	77.2491	87	1091	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_002250055.1	s__Sutcliffiella cohnii	77.248	106	1091	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_002860285.1	s__Peribacillus_A sp002860285	77.2147	144	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008855.1	s__Bacillus_BT aquiflavi	77.201	90	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.1959	104	1091	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_001591565.1	s__Priestia flexa	77.1927	77	1091	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_018613035.1	s__Cytobacillus sp018613035	77.171	116	1091	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_008923245.1	s__Cytobacillus depressus	77.1143	106	1091	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_000829435.1	s__Jeotgalibacillus soli	77.0507	57	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844575.1	s__Margalitia camelliae	76.887	60	1091	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_011393025.1	s__URHB0009 sp011393025	76.8202	85	1091	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_008764295.1	s__Robertmurraya methanolica_A	76.7296	70	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.93	99.93	0.84	0.82	3	-
GCF_016107705.1	s__Neobacillus cucumis_B	76.7048	107	1091	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_006546985.1	s__VATK01 sp006546985	76.6873	88	1091	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_005502275.1	s__Robertmurraya siralis	76.627	94	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:49,719] [INFO] GTDB search result was written to GCF_009466385.1_ASM946638v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:49,720] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:49,730] [INFO] DFAST_QC result json was written to GCF_009466385.1_ASM946638v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:49,730] [INFO] DFAST_QC completed!
[2024-01-25 17:37:49,731] [INFO] Total running time: 0h1m14s