[2024-01-24 13:32:56,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference
[2024-01-24 13:32:57,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,475] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg062e4e7c-5080-4f8f-b8a5-e7e0ea07fc86/GCF_000406145.1_DDA898_1.0_genomic.fna.gz | prodigal -d GCF_000406145.1_DDA898_1.0_genomic.fna/cds.fna -a GCF_000406145.1_DDA898_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:12,967] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:12,967] [INFO] Task started: HMMsearch
[2024-01-24 13:33:12,968] [INFO] Running command: hmmsearch --tblout GCF_000406145.1_DDA898_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/reference_markers.hmm GCF_000406145.1_DDA898_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:13,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:13,244] [INFO] Found 6/6 markers.
[2024-01-24 13:33:13,286] [INFO] Query marker FASTA was written to GCF_000406145.1_DDA898_1.0_genomic.fna/markers.fasta
[2024-01-24 13:33:13,286] [INFO] Task started: Blastn
[2024-01-24 13:33:13,286] [INFO] Running command: blastn -query GCF_000406145.1_DDA898_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/reference_markers.fasta -out GCF_000406145.1_DDA898_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,146] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:14,146] [INFO] Target genome list was writen to GCF_000406145.1_DDA898_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:33:14,163] [INFO] Task started: fastANI
[2024-01-24 13:33:14,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg062e4e7c-5080-4f8f-b8a5-e7e0ea07fc86/GCF_000406145.1_DDA898_1.0_genomic.fna.gz --refList GCF_000406145.1_DDA898_1.0_genomic.fna/target_genomes.txt --output GCF_000406145.1_DDA898_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:30,021] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:30,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:30,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:30,033] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:30,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:30,033] [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=NCPPB 898	GCA_000406145.1	204038	204038	type	True	100.0	1624	1642	95	conclusive
Dickeya dadantii	strain=DSM 18020	GCA_003049785.1	204038	204038	type	True	99.9497	1598	1642	95	conclusive
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	96.6451	1409	1642	95	conclusive
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	94.2157	1404	1642	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	94.169	1423	1642	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	92.6289	1411	1642	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	92.6196	1398	1642	95	below_threshold
Dickeya dianthicola	strain=NCPPB 453	GCA_000365305.1	204039	204039	type	True	92.0498	1304	1642	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	81.1581	848	1642	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.5432	580	1642	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.5343	577	1642	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.4338	554	1642	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.2315	587	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:30,035] [INFO] DFAST Taxonomy check result was written to GCF_000406145.1_DDA898_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:33:30,036] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:30,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:30,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/checkm_data
[2024-01-24 13:33:30,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:30,085] [INFO] Task started: CheckM
[2024-01-24 13:33:30,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000406145.1_DDA898_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000406145.1_DDA898_1.0_genomic.fna/checkm_input GCF_000406145.1_DDA898_1.0_genomic.fna/checkm_result
[2024-01-24 13:34:14,650] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:14,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:14,669] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:14,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:14,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000406145.1_DDA898_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:34:14,670] [INFO] Task started: Blastn
[2024-01-24 13:34:14,670] [INFO] Running command: blastn -query GCF_000406145.1_DDA898_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb97ac16-0253-46d5-8cc9-f144e3bb9faa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000406145.1_DDA898_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:15,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:15,812] [INFO] Selected 6 target genomes.
[2024-01-24 13:34:15,813] [INFO] Target genome list was writen to GCF_000406145.1_DDA898_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:15,822] [INFO] Task started: fastANI
[2024-01-24 13:34:15,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg062e4e7c-5080-4f8f-b8a5-e7e0ea07fc86/GCF_000406145.1_DDA898_1.0_genomic.fna.gz --refList GCF_000406145.1_DDA898_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000406145.1_DDA898_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:23,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:23,488] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:23,488] [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	100.0	1624	1642	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	94.2157	1404	1642	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	92.6289	1411	1642	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	92.0498	1304	1642	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	89.6122	1250	1642	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	87.558	1242	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,489] [INFO] GTDB search result was written to GCF_000406145.1_DDA898_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:23,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:23,494] [INFO] DFAST_QC result json was written to GCF_000406145.1_DDA898_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:34:23,494] [INFO] DFAST_QC completed!
[2024-01-24 13:34:23,494] [INFO] Total running time: 0h1m27s