[2024-01-24 12:31:04,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference
[2024-01-24 12:31:05,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,908] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2b449d6-0635-4cfe-b435-bdd47b842f09/GCF_007725405.1_ASM772540v1_genomic.fna.gz | prodigal -d GCF_007725405.1_ASM772540v1_genomic.fna/cds.fna -a GCF_007725405.1_ASM772540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:15,288] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:15,289] [INFO] Task started: HMMsearch
[2024-01-24 12:31:15,289] [INFO] Running command: hmmsearch --tblout GCF_007725405.1_ASM772540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/reference_markers.hmm GCF_007725405.1_ASM772540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:15,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:15,578] [INFO] Found 6/6 markers.
[2024-01-24 12:31:15,628] [INFO] Query marker FASTA was written to GCF_007725405.1_ASM772540v1_genomic.fna/markers.fasta
[2024-01-24 12:31:15,628] [INFO] Task started: Blastn
[2024-01-24 12:31:15,628] [INFO] Running command: blastn -query GCF_007725405.1_ASM772540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/reference_markers.fasta -out GCF_007725405.1_ASM772540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:16,230] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:16,235] [INFO] Selected 33 target genomes.
[2024-01-24 12:31:16,236] [INFO] Target genome list was writen to GCF_007725405.1_ASM772540v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:16,865] [INFO] Task started: fastANI
[2024-01-24 12:31:16,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b449d6-0635-4cfe-b435-bdd47b842f09/GCF_007725405.1_ASM772540v1_genomic.fna.gz --refList GCF_007725405.1_ASM772540v1_genomic.fna/target_genomes.txt --output GCF_007725405.1_ASM772540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:37,762] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:37,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:37,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:37,780] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:37,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:37,781] [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 alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	79.8172	75	1416	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	79.723	58	1416	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	79.5124	64	1416	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	79.4996	78	1416	95	below_threshold
Alkalihalobacillus xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	78.6601	301	1416	95	below_threshold
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.6172	251	1416	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.5648	81	1416	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	77.4586	50	1416	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.4168	70	1416	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.2699	86	1416	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.1556	84	1416	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.1088	83	1416	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	77.0554	68	1416	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.7782	80	1416	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.771	75	1416	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.7254	73	1416	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.579	54	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:37,783] [INFO] DFAST Taxonomy check result was written to GCF_007725405.1_ASM772540v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:37,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:37,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:37,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/checkm_data
[2024-01-24 12:31:37,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:37,831] [INFO] Task started: CheckM
[2024-01-24 12:31:37,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007725405.1_ASM772540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007725405.1_ASM772540v1_genomic.fna/checkm_input GCF_007725405.1_ASM772540v1_genomic.fna/checkm_result
[2024-01-24 12:32:10,705] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:10,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,732] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:10,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:10,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007725405.1_ASM772540v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:10,733] [INFO] Task started: Blastn
[2024-01-24 12:32:10,733] [INFO] Running command: blastn -query GCF_007725405.1_ASM772540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06540bfa-8a47-4b93-af4f-d7a69e39b19d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007725405.1_ASM772540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,570] [INFO] Selected 21 target genomes.
[2024-01-24 12:32:11,570] [INFO] Target genome list was writen to GCF_007725405.1_ASM772540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:11,644] [INFO] Task started: fastANI
[2024-01-24 12:32:11,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b449d6-0635-4cfe-b435-bdd47b842f09/GCF_007725405.1_ASM772540v1_genomic.fna.gz --refList GCF_007725405.1_ASM772540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007725405.1_ASM772540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:27,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:27,840] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:27,840] [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_007725405.1	s__Bacillus_H miscanthi	100.0	1411	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	conclusive
GCF_002019765.1	s__Bacillus_H oshimensis	91.0934	1216	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	-
GCF_900177675.1	s__Neobacillus sp900177675	80.4456	56	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_900197585.1	s__Bacillus_H sp900197585	80.3131	608	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002276165.1	s__Cytobacillus kochii	79.4985	53	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_002109385.1	s__Bacillus_L krulwichiae	79.3217	77	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	78.8164	86	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_016907895.1	s__Bacillus_H xiaoxiensis	78.6612	301	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCF_002019705.1	s__Bacillus_H patagoniensis	78.5923	252	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598215.1	s__Bacillus_H clausii_B	77.7336	137	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.35	99.35	0.94	0.94	2	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	77.5766	52	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.2565	88	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	76.901	67	1416	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,842] [INFO] GTDB search result was written to GCF_007725405.1_ASM772540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:27,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:27,847] [INFO] DFAST_QC result json was written to GCF_007725405.1_ASM772540v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:27,847] [INFO] DFAST_QC completed!
[2024-01-24 12:32:27,847] [INFO] Total running time: 0h1m23s