[2024-01-24 13:57:00,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference
[2024-01-24 13:57:01,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:01,877] [INFO] Task started: Prodigal
[2024-01-24 13:57:01,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b303e72-8fa0-498a-82f3-f7922abc03bf/GCF_025660475.1_ASM2566047v1_genomic.fna.gz | prodigal -d GCF_025660475.1_ASM2566047v1_genomic.fna/cds.fna -a GCF_025660475.1_ASM2566047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:09,720] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:09,720] [INFO] Task started: HMMsearch
[2024-01-24 13:57:09,720] [INFO] Running command: hmmsearch --tblout GCF_025660475.1_ASM2566047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/reference_markers.hmm GCF_025660475.1_ASM2566047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:10,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:10,083] [INFO] Found 6/6 markers.
[2024-01-24 13:57:10,117] [INFO] Query marker FASTA was written to GCF_025660475.1_ASM2566047v1_genomic.fna/markers.fasta
[2024-01-24 13:57:10,118] [INFO] Task started: Blastn
[2024-01-24 13:57:10,118] [INFO] Running command: blastn -query GCF_025660475.1_ASM2566047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/reference_markers.fasta -out GCF_025660475.1_ASM2566047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:10,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:10,766] [INFO] Selected 34 target genomes.
[2024-01-24 13:57:10,766] [INFO] Target genome list was writen to GCF_025660475.1_ASM2566047v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:10,778] [INFO] Task started: fastANI
[2024-01-24 13:57:10,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b303e72-8fa0-498a-82f3-f7922abc03bf/GCF_025660475.1_ASM2566047v1_genomic.fna.gz --refList GCF_025660475.1_ASM2566047v1_genomic.fna/target_genomes.txt --output GCF_025660475.1_ASM2566047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:31,593] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:31,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:31,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:31,613] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:31,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:31,613] [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 andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	77.3903	151	1207	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.0209	76	1207	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	77.008	77	1207	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	76.9737	105	1207	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.8697	56	1207	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	76.8129	82	1207	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.7706	99	1207	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	76.7558	115	1207	95	below_threshold
Caldibacillus pasinlerensis	strain=P1	GCA_009996845.1	2703818	2703818	type	True	76.7135	131	1207	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	76.6927	71	1207	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	76.6912	76	1207	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.6075	67	1207	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.5981	93	1207	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.594	71	1207	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.5771	75	1207	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.472	57	1207	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.4593	77	1207	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.4293	71	1207	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.4113	81	1207	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	76.4063	59	1207	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.3878	80	1207	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	76.2858	51	1207	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	76.2336	55	1207	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.1954	73	1207	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	75.937	54	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:31,615] [INFO] DFAST Taxonomy check result was written to GCF_025660475.1_ASM2566047v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:31,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:31,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:31,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/checkm_data
[2024-01-24 13:57:31,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:31,654] [INFO] Task started: CheckM
[2024-01-24 13:57:31,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025660475.1_ASM2566047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025660475.1_ASM2566047v1_genomic.fna/checkm_input GCF_025660475.1_ASM2566047v1_genomic.fna/checkm_result
[2024-01-24 13:58:00,326] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:00,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:00,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:00,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:00,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025660475.1_ASM2566047v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:00,351] [INFO] Task started: Blastn
[2024-01-24 13:58:00,352] [INFO] Running command: blastn -query GCF_025660475.1_ASM2566047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfca0262-7f99-4f27-9253-e93f27ac75c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_025660475.1_ASM2566047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:01,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:01,184] [INFO] Selected 35 target genomes.
[2024-01-24 13:58:01,184] [INFO] Target genome list was writen to GCF_025660475.1_ASM2566047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:01,204] [INFO] Task started: fastANI
[2024-01-24 13:58:01,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b303e72-8fa0-498a-82f3-f7922abc03bf/GCF_025660475.1_ASM2566047v1_genomic.fna.gz --refList GCF_025660475.1_ASM2566047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025660475.1_ASM2566047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:26,675] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:26,697] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:26,698] [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_001244735.1	s__Bacillus_J andreraoultii	77.4307	149	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_002797375.1	s__FJAT-46582 sp002797375	77.0611	66	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	96.55	96.55	0.91	0.91	2	-
GCF_000291355.1	s__Bacillus_A cereus_O	77.0431	63	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.56	96.56	0.88	0.83	4	-
GCF_013200995.1	s__Gottfriedia sp002556365	76.9524	60	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	95.58	95.58	0.84	0.83	3	-
GCF_902829255.1	s__Metabacillus niabensis	76.9	87	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_000751775.1	s__Bacillus_J thermoamylovorans	76.8633	140	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	98.31	97.86	0.86	0.85	9	-
GCA_902796085.1	s__RUG14133 sp902796085	76.856	113	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__RUG14133	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	76.7882	83	1207	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	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.7856	111	1207	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_002019635.1	s__Metabacillus halosaccharovorans	76.7505	100	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_009996845.1	s__RUG14133 sp009996845	76.6959	132	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__RUG14133	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923245.1	s__Cytobacillus depressus	76.6621	72	1207	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_000380245.2	s__Bacillus_AD massiliogorillae	76.6067	74	1207	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_002585305.1	s__Neobacillus sp002585305	76.5875	82	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_001420595.1	s__Cytobacillus solani	76.5748	94	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_001583695.1	s__Bacillus_A wiedmannii	76.5647	55	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.52	95.09	0.90	0.85	225	-
GCF_004006295.1	s__Peribacillus asahii_A	76.5462	72	1207	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_018332475.1	s__Bacillus_A sp018332475	76.5352	58	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.31	95.31	0.87	0.87	2	-
GCF_008923725.1	s__Bacillus_A sp008923725	76.4822	67	1207	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_002560985.1	s__Bacillus_A sp002560985	76.4795	74	1207	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_900094905.1	s__Bacillus_A cereus_AG	76.4709	57	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.51	99.13	0.92	0.90	3	-
GCF_008180335.1	s__Priestia megaterium_B	76.4364	83	1207	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_003570725.1	s__Peribacillus asahii	76.4293	71	1207	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_002156865.1	s__Gottfriedia luciferensis	76.4105	79	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772965.1	s__Ureibacillus massiliensis	76.3828	54	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006546985.1	s__VATK01 sp006546985	76.3505	80	1207	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_009928415.1	s__Neobacillus sp009928415	76.2892	85	1207	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	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	76.1737	73	1207	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_018613065.1	s__Neobacillus sp018613065	76.1437	75	1207	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:26,700] [INFO] GTDB search result was written to GCF_025660475.1_ASM2566047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:26,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:26,709] [INFO] DFAST_QC result json was written to GCF_025660475.1_ASM2566047v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:26,710] [INFO] DFAST_QC completed!
[2024-01-24 13:58:26,710] [INFO] Total running time: 0h1m26s