[2024-01-25 18:42:20,440] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference
[2024-01-25 18:42:21,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,540] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea103f2-bd0e-4ccb-82b5-63365558e8c0/GCF_003049785.1_ASM304978v1_genomic.fna.gz | prodigal -d GCF_003049785.1_ASM304978v1_genomic.fna/cds.fna -a GCF_003049785.1_ASM304978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:35,633] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:35,633] [INFO] Task started: HMMsearch
[2024-01-25 18:42:35,634] [INFO] Running command: hmmsearch --tblout GCF_003049785.1_ASM304978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/reference_markers.hmm GCF_003049785.1_ASM304978v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:35,895] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:35,897] [INFO] Found 6/6 markers.
[2024-01-25 18:42:35,944] [INFO] Query marker FASTA was written to GCF_003049785.1_ASM304978v1_genomic.fna/markers.fasta
[2024-01-25 18:42:35,944] [INFO] Task started: Blastn
[2024-01-25 18:42:35,944] [INFO] Running command: blastn -query GCF_003049785.1_ASM304978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/reference_markers.fasta -out GCF_003049785.1_ASM304978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:36,769] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:36,772] [INFO] Selected 13 target genomes.
[2024-01-25 18:42:36,773] [INFO] Target genome list was writen to GCF_003049785.1_ASM304978v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:36,777] [INFO] Task started: fastANI
[2024-01-25 18:42:36,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea103f2-bd0e-4ccb-82b5-63365558e8c0/GCF_003049785.1_ASM304978v1_genomic.fna.gz --refList GCF_003049785.1_ASM304978v1_genomic.fna/target_genomes.txt --output GCF_003049785.1_ASM304978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:52,200] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:52,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:52,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:52,210] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:42:52,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:52,210] [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
Dickeya dadantii	strain=DSM 18020	GCA_003049785.1	204038	204038	type	True	100.0	1665	1665	95	conclusive
Dickeya dadantii	strain=NCPPB 898	GCA_000406145.1	204038	204038	type	True	99.9455	1600	1665	95	conclusive
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	96.654	1446	1665	95	conclusive
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	94.2634	1464	1665	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	94.1801	1455	1665	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	92.7077	1451	1665	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	92.651	1432	1665	95	below_threshold
Dickeya dianthicola	strain=NCPPB 453	GCA_000365305.1	204039	204039	type	True	92.1119	1327	1665	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	81.1039	872	1665	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.7461	592	1665	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.6968	608	1665	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.5365	601	1665	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.5161	573	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:52,211] [INFO] DFAST Taxonomy check result was written to GCF_003049785.1_ASM304978v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:52,212] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:52,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:52,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/checkm_data
[2024-01-25 18:42:52,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:52,262] [INFO] Task started: CheckM
[2024-01-25 18:42:52,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049785.1_ASM304978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049785.1_ASM304978v1_genomic.fna/checkm_input GCF_003049785.1_ASM304978v1_genomic.fna/checkm_result
[2024-01-25 18:43:35,477] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:35,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:35,506] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:35,506] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:35,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049785.1_ASM304978v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:35,507] [INFO] Task started: Blastn
[2024-01-25 18:43:35,507] [INFO] Running command: blastn -query GCF_003049785.1_ASM304978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba04141-6269-4d34-bb02-c67bdc6b02b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049785.1_ASM304978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:36,754] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:36,757] [INFO] Selected 6 target genomes.
[2024-01-25 18:43:36,757] [INFO] Target genome list was writen to GCF_003049785.1_ASM304978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:36,765] [INFO] Task started: fastANI
[2024-01-25 18:43:36,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea103f2-bd0e-4ccb-82b5-63365558e8c0/GCF_003049785.1_ASM304978v1_genomic.fna.gz --refList GCF_003049785.1_ASM304978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049785.1_ASM304978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:45,113] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:45,119] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:45,119] [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_000406145.1	s__Dickeya dadantii	99.9455	1600	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	conclusive
GCF_001644705.1	s__Dickeya solani	94.2606	1463	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	-
GCF_002812485.1	s__Dickeya fangzhongdai	92.7057	1450	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCF_000365305.1	s__Dickeya dianthicola	92.1247	1327	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.46	97.48	0.95	0.91	50	-
GCF_000784735.1	s__Dickeya undicola	89.5531	1274	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.06	99.05	0.94	0.93	3	-
GCF_000406105.1	s__Dickeya chrysanthemi	87.6557	1256	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:45,120] [INFO] GTDB search result was written to GCF_003049785.1_ASM304978v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:45,121] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:45,123] [INFO] DFAST_QC result json was written to GCF_003049785.1_ASM304978v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:45,123] [INFO] DFAST_QC completed!
[2024-01-25 18:43:45,123] [INFO] Total running time: 0h1m25s