[2024-01-24 14:53:49,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:49,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:49,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference
[2024-01-24 14:53:50,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:50,323] [INFO] Task started: Prodigal
[2024-01-24 14:53:50,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg7efcaa8e-312e-4536-8f61-799342defdfa/GCF_004116265.1_ASM411626v1_genomic.fna.gz | prodigal -d GCF_004116265.1_ASM411626v1_genomic.fna/cds.fna -a GCF_004116265.1_ASM411626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:53:59,521] [INFO] Task succeeded: Prodigal
[2024-01-24 14:53:59,522] [INFO] Task started: HMMsearch
[2024-01-24 14:53:59,522] [INFO] Running command: hmmsearch --tblout GCF_004116265.1_ASM411626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/reference_markers.hmm GCF_004116265.1_ASM411626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:53:59,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:53:59,813] [INFO] Found 6/6 markers.
[2024-01-24 14:53:59,858] [INFO] Query marker FASTA was written to GCF_004116265.1_ASM411626v1_genomic.fna/markers.fasta
[2024-01-24 14:53:59,858] [INFO] Task started: Blastn
[2024-01-24 14:53:59,859] [INFO] Running command: blastn -query GCF_004116265.1_ASM411626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/reference_markers.fasta -out GCF_004116265.1_ASM411626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:00,460] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:00,464] [INFO] Selected 16 target genomes.
[2024-01-24 14:54:00,465] [INFO] Target genome list was writen to GCF_004116265.1_ASM411626v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:00,490] [INFO] Task started: fastANI
[2024-01-24 14:54:00,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg7efcaa8e-312e-4536-8f61-799342defdfa/GCF_004116265.1_ASM411626v1_genomic.fna.gz --refList GCF_004116265.1_ASM411626v1_genomic.fna/target_genomes.txt --output GCF_004116265.1_ASM411626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:15,115] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:15,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:15,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:15,126] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:15,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:15,126] [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
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	100.0	1614	1617	95	conclusive
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	79.4999	614	1617	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	78.5769	314	1617	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	78.4073	304	1617	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	77.9696	313	1617	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.9466	85	1617	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.826	57	1617	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	76.8175	138	1617	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.7086	114	1617	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.641	55	1617	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.6403	74	1617	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.3652	87	1617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:15,128] [INFO] DFAST Taxonomy check result was written to GCF_004116265.1_ASM411626v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:15,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:15,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:15,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/checkm_data
[2024-01-24 14:54:15,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:15,176] [INFO] Task started: CheckM
[2024-01-24 14:54:15,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116265.1_ASM411626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116265.1_ASM411626v1_genomic.fna/checkm_input GCF_004116265.1_ASM411626v1_genomic.fna/checkm_result
[2024-01-24 14:54:47,816] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:47,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:47,840] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:47,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:47,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116265.1_ASM411626v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:47,841] [INFO] Task started: Blastn
[2024-01-24 14:54:47,841] [INFO] Running command: blastn -query GCF_004116265.1_ASM411626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb449be-9236-4777-8bd9-14849054b870/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116265.1_ASM411626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:48,630] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:48,634] [INFO] Selected 16 target genomes.
[2024-01-24 14:54:48,634] [INFO] Target genome list was writen to GCF_004116265.1_ASM411626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:48,650] [INFO] Task started: fastANI
[2024-01-24 14:54:48,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg7efcaa8e-312e-4536-8f61-799342defdfa/GCF_004116265.1_ASM411626v1_genomic.fna.gz --refList GCF_004116265.1_ASM411626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116265.1_ASM411626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:03,808] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:03,821] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:03,821] [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_004116265.1	s__Anaerobacillus alkaliphilus	100.0	1614	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001866075.3	s__Anaerobacillus isosaccharinicus	79.5034	614	1617	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_001866055.1	s__Anaerobacillus alkalidiazotrophicus	78.6192	313	1617	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_001866005.1	s__Anaerobacillus alkalilacustris	78.4186	302	1617	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_001865995.1	s__Anaerobacillus arseniciselenatis	77.9696	313	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120055.1	s__Anaerobacillus sp007120055	77.5248	233	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118195.1	s__Anaerobacillus sp007118195	77.5182	241	1617	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_002797395.1	s__45385 sp002797395	76.9721	90	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	76.9002	85	1617	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_014138605.1	s__Peribacillus huizhouensis	76.7986	60	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	98.72	98.72	0.94	0.94	2	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	76.6486	71	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551815.1	s__Bacillus_A sp002551815	75.9731	63	1617	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:03,822] [INFO] GTDB search result was written to GCF_004116265.1_ASM411626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:03,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:03,829] [INFO] DFAST_QC result json was written to GCF_004116265.1_ASM411626v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:03,829] [INFO] DFAST_QC completed!
[2024-01-24 14:55:03,829] [INFO] Total running time: 0h1m15s