[2024-01-24 12:23:02,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:02,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:02,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference
[2024-01-24 12:23:04,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,107] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,107] [INFO] Running command: gunzip -c /var/lib/cwl/stgde15b406-d2be-4101-9e15-6a5ef983bcd9/GCF_000971155.1_ASM97115v1_genomic.fna.gz | prodigal -d GCF_000971155.1_ASM97115v1_genomic.fna/cds.fna -a GCF_000971155.1_ASM97115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:11,673] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:11,673] [INFO] Task started: HMMsearch
[2024-01-24 12:23:11,673] [INFO] Running command: hmmsearch --tblout GCF_000971155.1_ASM97115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/reference_markers.hmm GCF_000971155.1_ASM97115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:11,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:11,889] [INFO] Found 6/6 markers.
[2024-01-24 12:23:11,915] [INFO] Query marker FASTA was written to GCF_000971155.1_ASM97115v1_genomic.fna/markers.fasta
[2024-01-24 12:23:11,915] [INFO] Task started: Blastn
[2024-01-24 12:23:11,915] [INFO] Running command: blastn -query GCF_000971155.1_ASM97115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/reference_markers.fasta -out GCF_000971155.1_ASM97115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:13,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:13,215] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:13,215] [INFO] Target genome list was writen to GCF_000971155.1_ASM97115v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:13,234] [INFO] Task started: fastANI
[2024-01-24 12:23:13,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgde15b406-d2be-4101-9e15-6a5ef983bcd9/GCF_000971155.1_ASM97115v1_genomic.fna.gz --refList GCF_000971155.1_ASM97115v1_genomic.fna/target_genomes.txt --output GCF_000971155.1_ASM97115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:23,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:23,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:23,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:23,233] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:23,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:23,234] [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
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	100.0	977	978	95	conclusive
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	91.0334	883	978	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	87.0535	764	978	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	86.9036	795	978	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	86.5372	757	978	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	86.4485	741	978	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	86.3328	749	978	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	85.6997	745	978	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.538	429	978	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.0236	448	978	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.3182	320	978	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.1029	322	978	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.0558	194	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,235] [INFO] DFAST Taxonomy check result was written to GCF_000971155.1_ASM97115v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:23,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:23,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:23,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/checkm_data
[2024-01-24 12:23:23,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:23,271] [INFO] Task started: CheckM
[2024-01-24 12:23:23,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971155.1_ASM97115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971155.1_ASM97115v1_genomic.fna/checkm_input GCF_000971155.1_ASM97115v1_genomic.fna/checkm_result
[2024-01-24 12:24:00,071] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:00,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,090] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:00,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:00,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971155.1_ASM97115v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:00,091] [INFO] Task started: Blastn
[2024-01-24 12:24:00,092] [INFO] Running command: blastn -query GCF_000971155.1_ASM97115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24fab291-a1bd-42b2-bd42-eecbf9eee19b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971155.1_ASM97115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:02,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:02,533] [INFO] Selected 8 target genomes.
[2024-01-24 12:24:02,534] [INFO] Target genome list was writen to GCF_000971155.1_ASM97115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:02,537] [INFO] Task started: fastANI
[2024-01-24 12:24:02,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgde15b406-d2be-4101-9e15-6a5ef983bcd9/GCF_000971155.1_ASM97115v1_genomic.fna.gz --refList GCF_000971155.1_ASM97115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971155.1_ASM97115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:09,253] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:09,259] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:09,259] [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_000971155.1	s__Demequina maris	100.0	977	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	conclusive
GCF_000971255.1	s__Demequina rhizosphaerae	91.0334	883	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_000971215.1	s__Demequina silvatica	87.0896	762	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971135.1	s__Demequina phytophila	86.9321	793	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	86.5531	756	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759715.1	s__Demequina mangrovi	86.3598	748	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971235.1	s__Demequina subtropica	85.7	745	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971395.1	s__Demequina iriomotensis	85.6921	761	978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:09,261] [INFO] GTDB search result was written to GCF_000971155.1_ASM97115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:09,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:09,264] [INFO] DFAST_QC result json was written to GCF_000971155.1_ASM97115v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:09,264] [INFO] DFAST_QC completed!
[2024-01-24 12:24:09,264] [INFO] Total running time: 0h1m6s