[2024-01-24 14:46:35,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference
[2024-01-24 14:46:37,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,181] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,181] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb1df93b-736e-4854-a411-2756617f0814/GCF_003201975.1_ASM320197v1_genomic.fna.gz | prodigal -d GCF_003201975.1_ASM320197v1_genomic.fna/cds.fna -a GCF_003201975.1_ASM320197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:46,338] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:46,338] [INFO] Task started: HMMsearch
[2024-01-24 14:46:46,338] [INFO] Running command: hmmsearch --tblout GCF_003201975.1_ASM320197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/reference_markers.hmm GCF_003201975.1_ASM320197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:46,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:46,587] [INFO] Found 6/6 markers.
[2024-01-24 14:46:46,626] [INFO] Query marker FASTA was written to GCF_003201975.1_ASM320197v1_genomic.fna/markers.fasta
[2024-01-24 14:46:46,626] [INFO] Task started: Blastn
[2024-01-24 14:46:46,626] [INFO] Running command: blastn -query GCF_003201975.1_ASM320197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/reference_markers.fasta -out GCF_003201975.1_ASM320197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:47,244] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:47,248] [INFO] Selected 23 target genomes.
[2024-01-24 14:46:47,248] [INFO] Target genome list was writen to GCF_003201975.1_ASM320197v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:47,271] [INFO] Task started: fastANI
[2024-01-24 14:46:47,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb1df93b-736e-4854-a411-2756617f0814/GCF_003201975.1_ASM320197v1_genomic.fna.gz --refList GCF_003201975.1_ASM320197v1_genomic.fna/target_genomes.txt --output GCF_003201975.1_ASM320197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:02,146] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:02,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:02,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:02,161] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:02,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:02,161] [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
Pseudogracilibacillus auburnensis	strain=DSM 28556	GCA_003201975.1	1494959	1494959	type	True	100.0	1576	1576	95	conclusive
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.2282	66	1576	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	76.9904	71	1576	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	76.7571	95	1576	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.6907	97	1576	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	76.5988	54	1576	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.5922	88	1576	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.5864	95	1576	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	76.5352	97	1576	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.3488	53	1576	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	76.2643	90	1576	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.0891	51	1576	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	76.0022	68	1576	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	75.8749	67	1576	95	below_threshold
Salirhabdus euzebyi	strain=DSM 19612	GCA_014207435.1	394506	394506	type	True	75.8296	55	1576	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	75.1946	50	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:02,163] [INFO] DFAST Taxonomy check result was written to GCF_003201975.1_ASM320197v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:02,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:02,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:02,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/checkm_data
[2024-01-24 14:47:02,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:02,210] [INFO] Task started: CheckM
[2024-01-24 14:47:02,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201975.1_ASM320197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201975.1_ASM320197v1_genomic.fna/checkm_input GCF_003201975.1_ASM320197v1_genomic.fna/checkm_result
[2024-01-24 14:47:33,492] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:33,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:33,513] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:33,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:33,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201975.1_ASM320197v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:33,514] [INFO] Task started: Blastn
[2024-01-24 14:47:33,515] [INFO] Running command: blastn -query GCF_003201975.1_ASM320197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4d8104-3dff-43c0-b752-5a34869b686d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201975.1_ASM320197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:34,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:34,505] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:34,505] [INFO] Target genome list was writen to GCF_003201975.1_ASM320197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:34,522] [INFO] Task started: fastANI
[2024-01-24 14:47:34,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb1df93b-736e-4854-a411-2756617f0814/GCF_003201975.1_ASM320197v1_genomic.fna.gz --refList GCF_003201975.1_ASM320197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201975.1_ASM320197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:49,997] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:50,012] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:50,013] [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_003201975.1	s__Pseudogracilibacillus auburnensis	100.0	1576	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pseudogracilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000190475.1	s__Ornithinibacillus scapharcae	77.2154	66	1576	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_000340475.1	s__Oceanobacillus kimchii	76.9905	72	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_018075365.1	s__Virgibacillus pantothenticus	76.7571	95	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCA_019113205.1	s__Pseudogracilibacillus intestinigallinarum	76.6969	174	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pseudogracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007301515.1	s__Radiobacillus deserti	76.6371	55	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	76.5511	89	1576	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_900187325.1	s__Virgibacillus_E ndiopensis	76.5294	101	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	76.4638	82	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.4254	106	1576	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_016919725.1	s__Virgibacillus sp016919725	76.3416	91	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_005870085.1	s__BH258 sp005870085	76.3329	53	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612345.1	s__Virgibacillus sp003612345	76.2762	77	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	100.00	100.00	1.00	0.99	4	-
GCF_001368815.1	s__Paraliobacillus sp001368815	76.1874	62	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918075.1	s__MSJ-26 sp018918075	76.1091	95	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__MSJ-26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202495.1	s__Cerasibacillus quisquiliarum	76.0886	89	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001659985.1	s__Oceanobacillus sp001659985	76.0635	80	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009389585.1	s__Oceanobacillus sp009389585	75.9552	57	1576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:50,014] [INFO] GTDB search result was written to GCF_003201975.1_ASM320197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:50,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:50,019] [INFO] DFAST_QC result json was written to GCF_003201975.1_ASM320197v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:50,019] [INFO] DFAST_QC completed!
[2024-01-24 14:47:50,019] [INFO] Total running time: 0h1m14s