[2024-01-24 11:20:49,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,930] [INFO] DQC Reference Directory: /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference
[2024-01-24 11:20:51,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,161] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg33950bcb-5cfe-4eb6-9f0e-762c57df12a4/GCF_001039475.1_ASM103947v1_genomic.fna.gz | prodigal -d GCF_001039475.1_ASM103947v1_genomic.fna/cds.fna -a GCF_001039475.1_ASM103947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:00,180] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:00,181] [INFO] Task started: HMMsearch
[2024-01-24 11:21:00,181] [INFO] Running command: hmmsearch --tblout GCF_001039475.1_ASM103947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/reference_markers.hmm GCF_001039475.1_ASM103947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:00,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:00,444] [INFO] Found 6/6 markers.
[2024-01-24 11:21:00,482] [INFO] Query marker FASTA was written to GCF_001039475.1_ASM103947v1_genomic.fna/markers.fasta
[2024-01-24 11:21:00,483] [INFO] Task started: Blastn
[2024-01-24 11:21:00,483] [INFO] Running command: blastn -query GCF_001039475.1_ASM103947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/reference_markers.fasta -out GCF_001039475.1_ASM103947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:01,054] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:01,057] [INFO] Selected 22 target genomes.
[2024-01-24 11:21:01,057] [INFO] Target genome list was writen to GCF_001039475.1_ASM103947v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:01,149] [INFO] Task started: fastANI
[2024-01-24 11:21:01,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg33950bcb-5cfe-4eb6-9f0e-762c57df12a4/GCF_001039475.1_ASM103947v1_genomic.fna.gz --refList GCF_001039475.1_ASM103947v1_genomic.fna/target_genomes.txt --output GCF_001039475.1_ASM103947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:18,688] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:18,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:18,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:18,705] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:18,705] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:18,705] [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
Alkalihalobacillus macyae	strain=DSM 16346	GCA_001039475.1	157733	157733	type	True	100.0	1410	1410	95	conclusive
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	76.605	53	1410	95	below_threshold
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	76.5725	66	1410	95	below_threshold
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	76.4717	64	1410	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.3485	56	1410	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.1876	58	1410	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	76.0097	60	1410	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	75.8166	59	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:18,708] [INFO] DFAST Taxonomy check result was written to GCF_001039475.1_ASM103947v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:18,708] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:18,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:18,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/checkm_data
[2024-01-24 11:21:18,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:18,751] [INFO] Task started: CheckM
[2024-01-24 11:21:18,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001039475.1_ASM103947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001039475.1_ASM103947v1_genomic.fna/checkm_input GCF_001039475.1_ASM103947v1_genomic.fna/checkm_result
[2024-01-24 11:21:50,789] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:50,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:50,812] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:50,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:50,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001039475.1_ASM103947v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:50,813] [INFO] Task started: Blastn
[2024-01-24 11:21:50,813] [INFO] Running command: blastn -query GCF_001039475.1_ASM103947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c0d1bc-cd7e-4c06-8705-01af416a4368/dqc_reference/reference_markers_gtdb.fasta -out GCF_001039475.1_ASM103947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:51,536] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:51,540] [INFO] Selected 8 target genomes.
[2024-01-24 11:21:51,541] [INFO] Target genome list was writen to GCF_001039475.1_ASM103947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:51,548] [INFO] Task started: fastANI
[2024-01-24 11:21:51,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg33950bcb-5cfe-4eb6-9f0e-762c57df12a4/GCF_001039475.1_ASM103947v1_genomic.fna.gz --refList GCF_001039475.1_ASM103947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001039475.1_ASM103947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:00,290] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:00,302] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:00,303] [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_001039475.1	s__Anaerobacillus_A macyae	100.0	1410	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	87.5807	1164	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303315.1	s__Anaerobacillus_A sp017303315	87.3843	1122	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234585.1	s__Anaerobacillus_A hwajinpoensis_B	81.0586	756	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563635.1	s__Anaerobacillus_A sp002563635	81.016	718	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	96.09	95.80	0.90	0.90	3	-
GCF_009818105.1	s__Anaerobacillus_A sp009818105	80.9802	701	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016401385.1	s__Fictibacillus halophilus	76.6911	65	1410	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:00,304] [INFO] GTDB search result was written to GCF_001039475.1_ASM103947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:00,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:00,308] [INFO] DFAST_QC result json was written to GCF_001039475.1_ASM103947v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:00,308] [INFO] DFAST_QC completed!
[2024-01-24 11:22:00,308] [INFO] Total running time: 0h1m10s