[2024-01-24 12:13:04,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:04,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:04,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference
[2024-01-24 12:13:05,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:05,927] [INFO] Task started: Prodigal
[2024-01-24 12:13:05,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgee4dd46a-6f98-47ef-8468-bcc5ae3e449d/GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/cds.fna -a GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:15,884] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:15,885] [INFO] Task started: HMMsearch
[2024-01-24 12:13:15,885] [INFO] Running command: hmmsearch --tblout GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/reference_markers.hmm GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:16,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:16,143] [INFO] Found 6/6 markers.
[2024-01-24 12:13:16,183] [INFO] Query marker FASTA was written to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:16,184] [INFO] Task started: Blastn
[2024-01-24 12:13:16,184] [INFO] Running command: blastn -query GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/reference_markers.fasta -out GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:16,820] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:16,824] [INFO] Selected 19 target genomes.
[2024-01-24 12:13:16,824] [INFO] Target genome list was writen to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:16,831] [INFO] Task started: fastANI
[2024-01-24 12:13:16,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4dd46a-6f98-47ef-8468-bcc5ae3e449d/GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna.gz --refList GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:30,687] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:30,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:30,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:30,702] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:30,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:30,703] [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 endophytica	strain=DSM 13796	GCA_900115845.1	135735	135735	type	True	100.0	1682	1686	95	conclusive
Priestia filamentosa	strain=DSM 27955	GCA_002237735.1	1402861	1402861	type	True	94.657	1445	1686	95	below_threshold
Priestia filamentosa	strain=SGD-14	GCA_900177535.1	1402861	1402861	type	True	94.6374	1447	1686	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	77.4287	157	1686	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	77.2567	101	1686	95	below_threshold
Bacillus safensis	strain=FO-36b	GCA_003097715.1	561879	561879	type	True	77.1837	89	1686	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	77.0377	119	1686	95	below_threshold
Rossellomorea aquimaris	strain=TF12	GCA_001648555.1	189382	189382	suspected-type	True	76.9545	85	1686	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	76.9225	71	1686	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.8209	120	1686	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.7902	93	1686	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	76.7751	115	1686	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	76.7266	129	1686	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	76.6985	71	1686	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.5078	98	1686	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.4885	91	1686	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.1026	67	1686	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	75.9729	73	1686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:30,704] [INFO] DFAST Taxonomy check result was written to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:30,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:30,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:30,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/checkm_data
[2024-01-24 12:13:30,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:30,754] [INFO] Task started: CheckM
[2024-01-24 12:13:30,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/checkm_input GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:04,180] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:04,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:04,199] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:04,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:04,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:04,200] [INFO] Task started: Blastn
[2024-01-24 12:14:04,201] [INFO] Running command: blastn -query GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg188995d5-f804-4454-b930-ba2fcf14b0d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:05,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:05,208] [INFO] Selected 22 target genomes.
[2024-01-24 12:14:05,209] [INFO] Target genome list was writen to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:05,226] [INFO] Task started: fastANI
[2024-01-24 12:14:05,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4dd46a-6f98-47ef-8468-bcc5ae3e449d/GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna.gz --refList GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:20,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:20,393] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:20,394] [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_900115845.1	s__Bacillus_I endophytica	100.0	1682	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	98.63	96.70	0.92	0.89	9	conclusive
GCF_900177535.1	s__Bacillus_I filamentosa	94.6572	1445	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	99.55	98.90	0.95	0.92	6	-
GCF_001590835.1	s__Bacillus_A gaemokensis	77.6382	144	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002584535.1	s__Bacillus_A cereus_AW	77.5963	131	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_008180335.1	s__Priestia megaterium_B	77.5557	159	1686	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_016909075.1	s__Priestia iocasae	77.4321	156	1686	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_001042485.2	s__Bacillus paralicheniformis	77.2484	67	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0745	98.70	96.39	0.96	0.84	103	-
GCF_016909175.1	s__Bacillus_AI deserti	77.2264	74	1686	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_001969855.1	s__Bacillus haynesii	77.1468	69	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_016908395.1	s__Metabacillus crassostreae	77.0994	120	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496285.1	s__Bacillus_A toyonensis	77.0673	110	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	96.74	0.93	0.83	279	-
GCF_003184905.1	s__Priestia sp003184905	76.9582	168	1686	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_001648555.1	s__Rossellomorea aquimaris	76.9262	85	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017425.1	s__Bacillus_A cytotoxicus	76.815	113	1686	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_000011645.1	s__Bacillus licheniformis	76.7595	71	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_001884135.1	s__Bacillus_A nitratireducens	76.7266	129	1686	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_900111345.1	s__Psychrobacillus sp900111345	76.647	55	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002574955.1	s__Bacillus_A cereus_AT	76.5452	130	1686	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_018588585.1	s__SM2101 sp018588585	76.4979	80	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SM2101;g__SM2101	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833605.1	s__Anoxybacillus ayderensis	76.2303	79	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCF_007676755.1	s__Psychrobacillus sp007676755	76.1974	51	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	76.1081	67	1686	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:20,395] [INFO] GTDB search result was written to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:20,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:20,400] [INFO] DFAST_QC result json was written to GCF_900115845.1_IMG-taxon_2599185264_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:20,400] [INFO] DFAST_QC completed!
[2024-01-24 12:14:20,400] [INFO] Total running time: 0h1m16s