[2024-01-24 11:20:19,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference
[2024-01-24 11:20:20,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,803] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,804] [INFO] Running command: gunzip -c /var/lib/cwl/stge531f924-f350-450c-9abf-aa3524e0ba79/GCF_014640535.1_ASM1464053v1_genomic.fna.gz | prodigal -d GCF_014640535.1_ASM1464053v1_genomic.fna/cds.fna -a GCF_014640535.1_ASM1464053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:32,614] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:32,615] [INFO] Task started: HMMsearch
[2024-01-24 11:20:32,615] [INFO] Running command: hmmsearch --tblout GCF_014640535.1_ASM1464053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/reference_markers.hmm GCF_014640535.1_ASM1464053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:32,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:32,961] [INFO] Found 6/6 markers.
[2024-01-24 11:20:32,999] [INFO] Query marker FASTA was written to GCF_014640535.1_ASM1464053v1_genomic.fna/markers.fasta
[2024-01-24 11:20:32,999] [INFO] Task started: Blastn
[2024-01-24 11:20:32,999] [INFO] Running command: blastn -query GCF_014640535.1_ASM1464053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/reference_markers.fasta -out GCF_014640535.1_ASM1464053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:34,244] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:34,248] [INFO] Selected 13 target genomes.
[2024-01-24 11:20:34,248] [INFO] Target genome list was writen to GCF_014640535.1_ASM1464053v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:34,274] [INFO] Task started: fastANI
[2024-01-24 11:20:34,274] [INFO] Running command: fastANI --query /var/lib/cwl/stge531f924-f350-450c-9abf-aa3524e0ba79/GCF_014640535.1_ASM1464053v1_genomic.fna.gz --refList GCF_014640535.1_ASM1464053v1_genomic.fna/target_genomes.txt --output GCF_014640535.1_ASM1464053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:44,830] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:44,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:44,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:44,846] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:44,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:44,847] [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
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	100.0	1446	1446	95	conclusive
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	99.9959	1444	1446	95	conclusive
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	81.1972	700	1446	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	81.1363	684	1446	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	80.7546	661	1446	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	80.3412	677	1446	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.2035	498	1446	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.1769	442	1446	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.1468	448	1446	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.1244	432	1446	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.1015	451	1446	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	78.5299	396	1446	95	below_threshold
Curtobacterium pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	78.5012	402	1446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:44,849] [INFO] DFAST Taxonomy check result was written to GCF_014640535.1_ASM1464053v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:44,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:44,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:44,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/checkm_data
[2024-01-24 11:20:44,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:44,896] [INFO] Task started: CheckM
[2024-01-24 11:20:44,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640535.1_ASM1464053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640535.1_ASM1464053v1_genomic.fna/checkm_input GCF_014640535.1_ASM1464053v1_genomic.fna/checkm_result
[2024-01-24 11:21:48,239] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:48,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:48,263] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:48,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:48,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640535.1_ASM1464053v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:48,264] [INFO] Task started: Blastn
[2024-01-24 11:21:48,264] [INFO] Running command: blastn -query GCF_014640535.1_ASM1464053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fbada68-76d4-4710-aca0-891708b5248e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640535.1_ASM1464053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:50,222] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:50,227] [INFO] Selected 11 target genomes.
[2024-01-24 11:21:50,227] [INFO] Target genome list was writen to GCF_014640535.1_ASM1464053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:50,239] [INFO] Task started: fastANI
[2024-01-24 11:21:50,240] [INFO] Running command: fastANI --query /var/lib/cwl/stge531f924-f350-450c-9abf-aa3524e0ba79/GCF_014640535.1_ASM1464053v1_genomic.fna.gz --refList GCF_014640535.1_ASM1464053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640535.1_ASM1464053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:59,568] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:59,584] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:59,585] [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_014640535.1	s__Cnuibacter physcomitrellae	100.0	1446	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cnuibacter	95.0	98.64	97.29	0.95	0.90	3	conclusive
GCF_015350805.1	s__Herbiconiux sp015350805	81.4493	688	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409865.1	s__Herbiconiux flava	81.1615	704	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_001571005.1	s__Herbiconiux solani	81.1109	686	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502775.1	s__Herbiconiux sp005502775	80.8966	657	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_013113715.1	s__Herbiconiux sp013113715	80.8928	731	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297105.1	s__Herbiconiux sp004297105	80.4833	631	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107435.1	s__Herbiconiux ginsengi	80.362	674	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384945.1	s__Clavibacter sp003384945	79.1852	442	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759585.1	s__Frigoribacterium endophyticum	78.9915	467	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_014842255.1	s__Frigoribacterium sp014842255	78.7211	402	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:59,586] [INFO] GTDB search result was written to GCF_014640535.1_ASM1464053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:59,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:59,597] [INFO] DFAST_QC result json was written to GCF_014640535.1_ASM1464053v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:59,598] [INFO] DFAST_QC completed!
[2024-01-24 11:21:59,598] [INFO] Total running time: 0h1m40s