[2024-01-24 11:13:49,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference
[2024-01-24 11:13:50,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,324] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c4b40b3-2b9b-4658-8962-034435afb52e/GCF_001644705.1_ASM164470v1_genomic.fna.gz | prodigal -d GCF_001644705.1_ASM164470v1_genomic.fna/cds.fna -a GCF_001644705.1_ASM164470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:06,537] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:06,537] [INFO] Task started: HMMsearch
[2024-01-24 11:14:06,538] [INFO] Running command: hmmsearch --tblout GCF_001644705.1_ASM164470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/reference_markers.hmm GCF_001644705.1_ASM164470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:06,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:06,834] [INFO] Found 6/6 markers.
[2024-01-24 11:14:06,875] [INFO] Query marker FASTA was written to GCF_001644705.1_ASM164470v1_genomic.fna/markers.fasta
[2024-01-24 11:14:06,875] [INFO] Task started: Blastn
[2024-01-24 11:14:06,875] [INFO] Running command: blastn -query GCF_001644705.1_ASM164470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/reference_markers.fasta -out GCF_001644705.1_ASM164470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:07,784] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:07,788] [INFO] Selected 13 target genomes.
[2024-01-24 11:14:07,789] [INFO] Target genome list was writen to GCF_001644705.1_ASM164470v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:07,795] [INFO] Task started: fastANI
[2024-01-24 11:14:07,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c4b40b3-2b9b-4658-8962-034435afb52e/GCF_001644705.1_ASM164470v1_genomic.fna.gz --refList GCF_001644705.1_ASM164470v1_genomic.fna/target_genomes.txt --output GCF_001644705.1_ASM164470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:22,797] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:22,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:22,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:22,812] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:14:22,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:22,812] [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 solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	100.0	1637	1639	95	conclusive
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	99.9623	1619	1639	95	conclusive
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	94.2815	1412	1639	95	below_threshold
Dickeya dadantii	strain=NCPPB 898	GCA_000406145.1	204038	204038	type	True	94.2623	1407	1639	95	below_threshold
Dickeya dadantii	strain=DSM 18020	GCA_003049785.1	204038	204038	type	True	94.2607	1466	1639	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	92.8514	1428	1639	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	92.8505	1459	1639	95	below_threshold
Dickeya dianthicola	strain=NCPPB 453	GCA_000365305.1	204039	204039	type	True	92.2338	1339	1639	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	81.2208	858	1639	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.6197	598	1639	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.5159	559	1639	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.4057	585	1639	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.6233	420	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:22,814] [INFO] DFAST Taxonomy check result was written to GCF_001644705.1_ASM164470v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:22,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:22,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:22,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/checkm_data
[2024-01-24 11:14:22,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:22,864] [INFO] Task started: CheckM
[2024-01-24 11:14:22,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001644705.1_ASM164470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001644705.1_ASM164470v1_genomic.fna/checkm_input GCF_001644705.1_ASM164470v1_genomic.fna/checkm_result
[2024-01-24 11:15:12,571] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:12,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:12,594] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:12,594] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:12,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001644705.1_ASM164470v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:12,595] [INFO] Task started: Blastn
[2024-01-24 11:15:12,595] [INFO] Running command: blastn -query GCF_001644705.1_ASM164470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3057a3d6-152e-4a91-b3aa-2cd20afbbcaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001644705.1_ASM164470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:14,058] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:14,062] [INFO] Selected 7 target genomes.
[2024-01-24 11:15:14,062] [INFO] Target genome list was writen to GCF_001644705.1_ASM164470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:14,082] [INFO] Task started: fastANI
[2024-01-24 11:15:14,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c4b40b3-2b9b-4658-8962-034435afb52e/GCF_001644705.1_ASM164470v1_genomic.fna.gz --refList GCF_001644705.1_ASM164470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001644705.1_ASM164470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:23,028] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:23,037] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:23,037] [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_001644705.1	s__Dickeya solani	100.0	1638	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	conclusive
GCF_000406145.1	s__Dickeya dadantii	94.2669	1406	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_002812485.1	s__Dickeya fangzhongdai	92.86	1460	1639	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	92.2471	1338	1639	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	89.5578	1275	1639	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	87.1738	1290	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
GCF_007858975.2	s__Dickeya poaceiphila	86.3819	1117	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.40	98.88	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:23,039] [INFO] GTDB search result was written to GCF_001644705.1_ASM164470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:23,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:23,042] [INFO] DFAST_QC result json was written to GCF_001644705.1_ASM164470v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:23,042] [INFO] DFAST_QC completed!
[2024-01-24 11:15:23,042] [INFO] Total running time: 0h1m34s