[2024-01-24 13:12:36,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:36,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:36,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference
[2024-01-24 13:12:37,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:37,602] [INFO] Task started: Prodigal
[2024-01-24 13:12:37,603] [INFO] Running command: gunzip -c /var/lib/cwl/stgdeadb5ec-b688-423d-9358-6447826d4ac4/GCF_001571045.1_ASM157104v1_genomic.fna.gz | prodigal -d GCF_001571045.1_ASM157104v1_genomic.fna/cds.fna -a GCF_001571045.1_ASM157104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:46,746] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:46,746] [INFO] Task started: HMMsearch
[2024-01-24 13:12:46,746] [INFO] Running command: hmmsearch --tblout GCF_001571045.1_ASM157104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/reference_markers.hmm GCF_001571045.1_ASM157104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:47,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:47,071] [INFO] Found 6/6 markers.
[2024-01-24 13:12:47,110] [INFO] Query marker FASTA was written to GCF_001571045.1_ASM157104v1_genomic.fna/markers.fasta
[2024-01-24 13:12:47,110] [INFO] Task started: Blastn
[2024-01-24 13:12:47,110] [INFO] Running command: blastn -query GCF_001571045.1_ASM157104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/reference_markers.fasta -out GCF_001571045.1_ASM157104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:48,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:48,418] [INFO] Selected 14 target genomes.
[2024-01-24 13:12:48,419] [INFO] Target genome list was writen to GCF_001571045.1_ASM157104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:48,425] [INFO] Task started: fastANI
[2024-01-24 13:12:48,426] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeadb5ec-b688-423d-9358-6447826d4ac4/GCF_001571045.1_ASM157104v1_genomic.fna.gz --refList GCF_001571045.1_ASM157104v1_genomic.fna/target_genomes.txt --output GCF_001571045.1_ASM157104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:58,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:58,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:58,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:58,543] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:12:58,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:58,544] [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
Curtobacterium ammoniigenes	strain=NBRC 101786	GCA_001571045.1	395387	395387	type	True	100.0	1007	1008	95	conclusive
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	79.8219	462	1008	95	below_threshold
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	79.8214	440	1008	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	79.7984	448	1008	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	79.779	440	1008	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	79.7432	437	1008	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	79.7422	427	1008	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	79.7405	458	1008	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	79.7217	458	1008	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	79.6889	454	1008	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	79.6882	437	1008	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	79.6261	444	1008	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.1358	244	1008	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.7794	262	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:58,545] [INFO] DFAST Taxonomy check result was written to GCF_001571045.1_ASM157104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:58,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:58,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:58,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/checkm_data
[2024-01-24 13:12:58,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:58,581] [INFO] Task started: CheckM
[2024-01-24 13:12:58,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001571045.1_ASM157104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001571045.1_ASM157104v1_genomic.fna/checkm_input GCF_001571045.1_ASM157104v1_genomic.fna/checkm_result
[2024-01-24 13:13:48,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:48,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,394] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:48,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:48,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001571045.1_ASM157104v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:48,395] [INFO] Task started: Blastn
[2024-01-24 13:13:48,395] [INFO] Running command: blastn -query GCF_001571045.1_ASM157104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg085ab733-97ec-49a6-8780-1891afe838ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_001571045.1_ASM157104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:50,059] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:50,062] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:50,062] [INFO] Target genome list was writen to GCF_001571045.1_ASM157104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:50,108] [INFO] Task started: fastANI
[2024-01-24 13:13:50,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeadb5ec-b688-423d-9358-6447826d4ac4/GCF_001571045.1_ASM157104v1_genomic.fna.gz --refList GCF_001571045.1_ASM157104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001571045.1_ASM157104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:02,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:02,190] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:02,190] [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_001571045.1	s__Curtobacterium ammoniigenes	100.0	1007	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001865065.1	s__Curtobacterium sp001865065	79.9686	441	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001475545.1	s__Curtobacterium luteum_A	79.855	425	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742745.1	s__Curtobacterium sp001742745	79.8436	440	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.38	97.38	0.89	0.89	2	-
GCF_001705035.1	s__Curtobacterium sp001705035	79.7281	416	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.77	98.72	0.93	0.91	3	-
GCF_006715175.1	s__Curtobacterium citreum	79.7018	460	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.94	96.06	0.93	0.88	10	-
GCF_002412165.1	s__Curtobacterium sp002412165	79.688	464	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025645.1	s__Curtobacterium pusillum_A	79.6866	467	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.99	95.99	0.91	0.91	2	-
GCF_014646995.1	s__Curtobacterium luteum	79.667	456	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	99.66	99.01	0.98	0.96	4	-
GCF_003224335.1	s__Curtobacterium sp003224335	79.6598	432	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	99.04	98.17	0.96	0.91	8	-
GCF_003762905.1	s__Curtobacterium sp003762905	79.6311	462	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.66	98.64	0.92	0.92	3	-
GCF_007673235.1	s__Curtobacterium pusillum_C	79.6199	467	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001864835.1	s__Curtobacterium sp001864835	79.6068	434	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900086645.1	s__Curtobacterium sp900086645	79.599	481	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234855.1	s__Curtobacterium sp003234855	79.5822	410	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613895.1	s__Curtobacterium sp018613895	79.5286	423	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422205.1	s__Curtobacterium sp001422205	79.4605	441	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	78.3565	247	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:02,192] [INFO] GTDB search result was written to GCF_001571045.1_ASM157104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:02,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:02,197] [INFO] DFAST_QC result json was written to GCF_001571045.1_ASM157104v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:02,198] [INFO] DFAST_QC completed!
[2024-01-24 13:14:02,198] [INFO] Total running time: 0h1m26s