[2024-01-24 15:10:23,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,132] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference
[2024-01-24 15:10:24,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg10a32433-80e3-4701-aa1e-86cfefd123ae/GCF_003429095.1_ASM342909v1_genomic.fna.gz | prodigal -d GCF_003429095.1_ASM342909v1_genomic.fna/cds.fna -a GCF_003429095.1_ASM342909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:34,361] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:34,362] [INFO] Task started: HMMsearch
[2024-01-24 15:10:34,362] [INFO] Running command: hmmsearch --tblout GCF_003429095.1_ASM342909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/reference_markers.hmm GCF_003429095.1_ASM342909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:34,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:34,649] [INFO] Found 6/6 markers.
[2024-01-24 15:10:34,689] [INFO] Query marker FASTA was written to GCF_003429095.1_ASM342909v1_genomic.fna/markers.fasta
[2024-01-24 15:10:34,690] [INFO] Task started: Blastn
[2024-01-24 15:10:34,690] [INFO] Running command: blastn -query GCF_003429095.1_ASM342909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/reference_markers.fasta -out GCF_003429095.1_ASM342909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:35,315] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:35,319] [INFO] Selected 29 target genomes.
[2024-01-24 15:10:35,320] [INFO] Target genome list was writen to GCF_003429095.1_ASM342909v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:35,335] [INFO] Task started: fastANI
[2024-01-24 15:10:35,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a32433-80e3-4701-aa1e-86cfefd123ae/GCF_003429095.1_ASM342909v1_genomic.fna.gz --refList GCF_003429095.1_ASM342909v1_genomic.fna/target_genomes.txt --output GCF_003429095.1_ASM342909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:54,349] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:54,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:54,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:54,367] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:54,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:54,368] [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
Peribacillus saganii	strain=V47-23a	GCA_003429095.1	2303992	2303992	type	True	100.0	1410	1416	95	conclusive
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	77.9323	103	1416	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.6721	147	1416	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.6694	77	1416	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	77.6141	119	1416	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.5209	114	1416	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.2082	60	1416	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.0961	91	1416	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.0104	58	1416	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.9973	101	1416	95	below_threshold
Jeotgalibacillus aurantiacus	strain=T12	GCA_020595125.1	2763266	2763266	type	True	76.99	51	1416	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	76.959	70	1416	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.9154	72	1416	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	76.9143	87	1416	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.855	103	1416	95	below_threshold
Domibacillus antri	strain=XD80	GCA_001936625.1	1714264	1714264	type	True	76.8045	50	1416	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.7944	67	1416	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	76.7734	93	1416	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	76.7357	65	1416	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	76.5546	86	1416	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.5213	88	1416	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.2756	64	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:54,370] [INFO] DFAST Taxonomy check result was written to GCF_003429095.1_ASM342909v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:54,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:54,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:54,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/checkm_data
[2024-01-24 15:10:54,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:54,418] [INFO] Task started: CheckM
[2024-01-24 15:10:54,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003429095.1_ASM342909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003429095.1_ASM342909v1_genomic.fna/checkm_input GCF_003429095.1_ASM342909v1_genomic.fna/checkm_result
[2024-01-24 15:11:28,102] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:28,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:28,123] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:28,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:28,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003429095.1_ASM342909v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:28,124] [INFO] Task started: Blastn
[2024-01-24 15:11:28,124] [INFO] Running command: blastn -query GCF_003429095.1_ASM342909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1ad42dd-f8a1-4f40-8d5f-c8d3d7453979/dqc_reference/reference_markers_gtdb.fasta -out GCF_003429095.1_ASM342909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,995] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:29,003] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:29,003] [INFO] Target genome list was writen to GCF_003429095.1_ASM342909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:29,034] [INFO] Task started: fastANI
[2024-01-24 15:11:29,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a32433-80e3-4701-aa1e-86cfefd123ae/GCF_003429095.1_ASM342909v1_genomic.fna.gz --refList GCF_003429095.1_ASM342909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003429095.1_ASM342909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:48,178] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:48,194] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:48,194] [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_003429095.1	s__Peribacillus_A saganii	100.0	1410	1416	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	conclusive
GCF_002860285.1	s__Peribacillus_A sp002860285	83.751	923	1416	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_002863565.1	s__Peribacillus sp002863565	78.2998	201	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112495.1	s__Peribacillus sp900112495	78.0838	148	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	95.26	95.26	0.85	0.85	2	-
GCF_000430765.1	s__Bacillus_AI kribbensis	77.9655	102	1416	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_001636425.1	s__Bacillus_AE acidicola	77.7681	77	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009466385.1	s__Bacillus_BN tepidiphilus	77.578	111	1416	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	77.2933	61	1416	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_002860255.1	s__Neobacillus cucumis_A	77.2312	97	1416	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_014874135.1	s__Neobacillus sp014874135	77.0884	103	1416	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_000724485.1	s__Bacillus_Z methanolicus_A	77.0584	90	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004366035.1	s__Cytobacillus oceanisediminis_C	77.0384	112	1416	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_001866655.1	s__Neobacillus sp001866655	77.0125	100	1416	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_000294775.2	s__Cytobacillus oceanisediminis_B	77.0073	136	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_018343665.1	s__Cytobacillus sp018343665	76.9899	115	1416	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_009849585.1	s__Cytobacillus sp009849585	76.8915	110	1416	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_017303275.1	s__Cytobacillus sp017303275	76.89	114	1416	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_000565285.1	s__Cytobacillus firmus_A	76.8542	106	1416	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_000262755.1	s__Bacillus_Z methanolicus	76.5754	84	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836495.1	s__Cytobacillus sp014836495	76.2756	64	1416	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:48,196] [INFO] GTDB search result was written to GCF_003429095.1_ASM342909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:48,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:48,201] [INFO] DFAST_QC result json was written to GCF_003429095.1_ASM342909v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:48,201] [INFO] DFAST_QC completed!
[2024-01-24 15:11:48,201] [INFO] Total running time: 0h1m25s