[2024-01-24 12:40:20,246] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,249] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,249] [INFO] DQC Reference Directory: /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference
[2024-01-24 12:40:21,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,447] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,447] [INFO] Running command: gunzip -c /var/lib/cwl/stgd52b29b6-26ed-40e3-8728-a8d64b74357e/GCF_000331575.1_ASM33157v1_genomic.fna.gz | prodigal -d GCF_000331575.1_ASM33157v1_genomic.fna/cds.fna -a GCF_000331575.1_ASM33157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:28,452] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:28,453] [INFO] Task started: HMMsearch
[2024-01-24 12:40:28,453] [INFO] Running command: hmmsearch --tblout GCF_000331575.1_ASM33157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/reference_markers.hmm GCF_000331575.1_ASM33157v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:28,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:28,712] [INFO] Found 6/6 markers.
[2024-01-24 12:40:28,754] [INFO] Query marker FASTA was written to GCF_000331575.1_ASM33157v1_genomic.fna/markers.fasta
[2024-01-24 12:40:28,755] [INFO] Task started: Blastn
[2024-01-24 12:40:28,755] [INFO] Running command: blastn -query GCF_000331575.1_ASM33157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/reference_markers.fasta -out GCF_000331575.1_ASM33157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:29,350] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:29,353] [INFO] Selected 29 target genomes.
[2024-01-24 12:40:29,353] [INFO] Target genome list was writen to GCF_000331575.1_ASM33157v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:29,363] [INFO] Task started: fastANI
[2024-01-24 12:40:29,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgd52b29b6-26ed-40e3-8728-a8d64b74357e/GCF_000331575.1_ASM33157v1_genomic.fna.gz --refList GCF_000331575.1_ASM33157v1_genomic.fna/target_genomes.txt --output GCF_000331575.1_ASM33157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:47,213] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:47,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:47,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:47,232] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:47,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:47,232] [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
Calidifontibacillus oryziterrae	strain=ZYK	GCA_000331575.1	1191699	1191699	type	True	100.0	1185	1185	95	conclusive
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	78.0054	235	1185	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	76.9279	84	1185	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.854	92	1185	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.7467	87	1185	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.7264	66	1185	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	76.6791	66	1185	95	below_threshold
Bacillus mesophilus	strain=SA4	GCA_011008845.1	1808955	1808955	type	True	76.6314	74	1185	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.6282	63	1185	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	76.5715	69	1185	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	76.5424	74	1185	95	below_threshold
Cytobacillus luteolus	strain=DSM 22388	GCA_017873715.1	682179	682179	type	True	76.4398	80	1185	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	76.4267	55	1185	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.419	81	1185	95	below_threshold
Cytobacillus luteolus	strain=YIM 93174	GCA_014982515.1	682179	682179	type	True	76.3061	84	1185	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.3051	66	1185	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	76.2683	76	1185	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.1511	61	1185	95	below_threshold
Lysinibacillus sphaericus	strain=KCTC 3346	GCA_000427235.1	1421	1421	suspected-type	True	75.7908	53	1185	95	below_threshold
Lysinibacillus sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	75.7852	51	1185	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	75.7595	50	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:47,234] [INFO] DFAST Taxonomy check result was written to GCF_000331575.1_ASM33157v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:47,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:47,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:47,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/checkm_data
[2024-01-24 12:40:47,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:47,278] [INFO] Task started: CheckM
[2024-01-24 12:40:47,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331575.1_ASM33157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331575.1_ASM33157v1_genomic.fna/checkm_input GCF_000331575.1_ASM33157v1_genomic.fna/checkm_result
[2024-01-24 12:41:13,999] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:14,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:14,020] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:14,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:14,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331575.1_ASM33157v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:14,021] [INFO] Task started: Blastn
[2024-01-24 12:41:14,021] [INFO] Running command: blastn -query GCF_000331575.1_ASM33157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb91670e7-26f3-4f8a-bddd-efa5b83ffcfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331575.1_ASM33157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:14,735] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:14,739] [INFO] Selected 22 target genomes.
[2024-01-24 12:41:14,740] [INFO] Target genome list was writen to GCF_000331575.1_ASM33157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:14,754] [INFO] Task started: fastANI
[2024-01-24 12:41:14,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgd52b29b6-26ed-40e3-8728-a8d64b74357e/GCF_000331575.1_ASM33157v1_genomic.fna.gz --refList GCF_000331575.1_ASM33157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000331575.1_ASM33157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:29,407] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:29,427] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:29,427] [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_000331575.1	s__Calidifontibacillus oryziterrae	100.0	1185	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016841285.1	s__Calidifontibacillus sp016841285	78.1799	195	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307855.1	s__Calidifontibacillus azotoformans	78.0188	234	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	97.05	97.05	0.89	0.89	2	-
GCA_012842745.1	s__Calidifontibacillus sp012842745	77.7866	253	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840465.1	s__Calidifontibacillus sp012840465	77.7726	229	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	77.6875	205	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	77.0525	82	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_018343515.1	s__Bacillus_AH sp018343515	76.9298	61	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008845.1	s__Bacillus_BS mesophilus	76.6575	75	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017873715.1	s__Bacillus_BV luteolus	76.4808	81	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002578045.1	s__Bacillus_A cereus_AK	76.4242	62	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.93	99.93	0.97	0.97	2	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	76.4121	80	1185	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	-
GCF_002559665.1	s__Bacillus_A cereus_AV	76.3726	68	1185	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_002577655.1	s__Metabacillus sp002577655	76.3463	86	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156865.1	s__Gottfriedia luciferensis	76.3051	66	1185	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_009728145.1	s__Ornithinibacillus caprae	76.145	52	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013314535.1	s__Bacillus_A sp013314535	76.142	63	1185	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:29,429] [INFO] GTDB search result was written to GCF_000331575.1_ASM33157v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:29,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:29,433] [INFO] DFAST_QC result json was written to GCF_000331575.1_ASM33157v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:29,433] [INFO] DFAST_QC completed!
[2024-01-24 12:41:29,433] [INFO] Total running time: 0h1m9s