[2024-01-24 12:13:26,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:26,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:26,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference
[2024-01-24 12:13:27,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:27,782] [INFO] Task started: Prodigal
[2024-01-24 12:13:27,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c539021-5922-4703-94ac-627e076c6268/GCF_004310685.1_ASM431068v1_genomic.fna.gz | prodigal -d GCF_004310685.1_ASM431068v1_genomic.fna/cds.fna -a GCF_004310685.1_ASM431068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:37,896] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:37,896] [INFO] Task started: HMMsearch
[2024-01-24 12:13:37,896] [INFO] Running command: hmmsearch --tblout GCF_004310685.1_ASM431068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/reference_markers.hmm GCF_004310685.1_ASM431068v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:38,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:38,200] [INFO] Found 6/6 markers.
[2024-01-24 12:13:38,227] [INFO] Query marker FASTA was written to GCF_004310685.1_ASM431068v1_genomic.fna/markers.fasta
[2024-01-24 12:13:38,227] [INFO] Task started: Blastn
[2024-01-24 12:13:38,227] [INFO] Running command: blastn -query GCF_004310685.1_ASM431068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/reference_markers.fasta -out GCF_004310685.1_ASM431068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:39,498] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:39,503] [INFO] Selected 24 target genomes.
[2024-01-24 12:13:39,503] [INFO] Target genome list was writen to GCF_004310685.1_ASM431068v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:39,533] [INFO] Task started: fastANI
[2024-01-24 12:13:39,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c539021-5922-4703-94ac-627e076c6268/GCF_004310685.1_ASM431068v1_genomic.fna.gz --refList GCF_004310685.1_ASM431068v1_genomic.fna/target_genomes.txt --output GCF_004310685.1_ASM431068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:54,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:54,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:54,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:54,461] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:13:54,461] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:13:54,461] [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
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	80.9834	549	1056	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	80.774	536	1056	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.4927	406	1056	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	79.2593	421	1056	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	79.2121	415	1056	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.1992	412	1056	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.1926	297	1056	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.0991	423	1056	95	below_threshold
Salinibacterium xinjiangense	strain=CGMCC 1.05381	GCA_900230175.1	386302	386302	type	True	79.0317	320	1056	95	below_threshold
Salinibacterium xinjiangense	strain=CGMCC 1.5381	GCA_014645015.1	386302	386302	type	True	79.0189	321	1056	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	78.9962	350	1056	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.9706	366	1056	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	78.9639	311	1056	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.9414	373	1056	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.9347	396	1056	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	78.7734	321	1056	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.7203	379	1056	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.7033	398	1056	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	78.6846	398	1056	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	78.6689	402	1056	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	78.6579	422	1056	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	78.6343	397	1056	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	78.6119	401	1056	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.5992	398	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:54,463] [INFO] DFAST Taxonomy check result was written to GCF_004310685.1_ASM431068v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:54,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:54,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:54,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/checkm_data
[2024-01-24 12:13:54,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:54,499] [INFO] Task started: CheckM
[2024-01-24 12:13:54,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310685.1_ASM431068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310685.1_ASM431068v1_genomic.fna/checkm_input GCF_004310685.1_ASM431068v1_genomic.fna/checkm_result
[2024-01-24 12:14:28,628] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:28,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,650] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:28,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:28,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310685.1_ASM431068v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:28,652] [INFO] Task started: Blastn
[2024-01-24 12:14:28,652] [INFO] Running command: blastn -query GCF_004310685.1_ASM431068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc4acfed-7e06-42ff-a11c-abb10d6de8d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310685.1_ASM431068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:30,600] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:30,603] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:30,603] [INFO] Target genome list was writen to GCF_004310685.1_ASM431068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:30,619] [INFO] Task started: fastANI
[2024-01-24 12:14:30,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c539021-5922-4703-94ac-627e076c6268/GCF_004310685.1_ASM431068v1_genomic.fna.gz --refList GCF_004310685.1_ASM431068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310685.1_ASM431068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:39,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:39,615] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:39,615] [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_004310685.1	s__Conyzicola arctica	100.0	1056	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014204935.1	s__Conyzicola lurida	80.9875	552	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639655.1	s__Conyzicola nivalis	80.8049	533	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	80.3335	497	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_013297645.1	s__JAAFHU01 sp013297645	80.2696	409	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920435.1	s__Rhodoglobus sp903920435	79.8622	455	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_014483895.1	s__Protaetiibacter sp014483895	79.2789	426	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217685.1	s__Lacisediminihabitans sp014217685	79.0977	377	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570845.1	s__Leifsonia_A flava	79.0123	389	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
GCF_016907835.1	s__Agromyces cerinus_A	78.9299	376	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716125.1	s__Homoserinimonas aerilata	78.9257	334	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Homoserinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	78.541	402	1056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:39,644] [INFO] GTDB search result was written to GCF_004310685.1_ASM431068v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:39,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:39,655] [INFO] DFAST_QC result json was written to GCF_004310685.1_ASM431068v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:39,655] [INFO] DFAST_QC completed!
[2024-01-24 12:14:39,655] [INFO] Total running time: 0h1m13s