[2024-01-24 15:35:23,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:35:23,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:35:23,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference
[2024-01-24 15:35:26,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:35:26,930] [INFO] Task started: Prodigal
[2024-01-24 15:35:26,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg606b4951-81bf-4d81-be20-335aa274384c/GCF_000767565.1_ASM76756v1_genomic.fna.gz | prodigal -d GCF_000767565.1_ASM76756v1_genomic.fna/cds.fna -a GCF_000767565.1_ASM76756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:35:34,998] [INFO] Task succeeded: Prodigal
[2024-01-24 15:35:34,999] [INFO] Task started: HMMsearch
[2024-01-24 15:35:34,999] [INFO] Running command: hmmsearch --tblout GCF_000767565.1_ASM76756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/reference_markers.hmm GCF_000767565.1_ASM76756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:35:35,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:35:35,234] [INFO] Found 6/6 markers.
[2024-01-24 15:35:35,258] [INFO] Query marker FASTA was written to GCF_000767565.1_ASM76756v1_genomic.fna/markers.fasta
[2024-01-24 15:35:35,258] [INFO] Task started: Blastn
[2024-01-24 15:35:35,259] [INFO] Running command: blastn -query GCF_000767565.1_ASM76756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/reference_markers.fasta -out GCF_000767565.1_ASM76756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:35:35,943] [INFO] Task succeeded: Blastn
[2024-01-24 15:35:35,947] [INFO] Selected 10 target genomes.
[2024-01-24 15:35:35,947] [INFO] Target genome list was writen to GCF_000767565.1_ASM76756v1_genomic.fna/target_genomes.txt
[2024-01-24 15:35:35,956] [INFO] Task started: fastANI
[2024-01-24 15:35:35,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg606b4951-81bf-4d81-be20-335aa274384c/GCF_000767565.1_ASM76756v1_genomic.fna.gz --refList GCF_000767565.1_ASM76756v1_genomic.fna/target_genomes.txt --output GCF_000767565.1_ASM76756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:35:42,352] [INFO] Task succeeded: fastANI
[2024-01-24 15:35:42,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:35:42,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:35:42,359] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:35:42,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:35:42,360] [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
Xylella fastidiosa	strain=ATCC 35879	GCA_000767565.1	2371	2371	type	True	100.0	829	833	95	conclusive
Xylella fastidiosa	strain=ATCC 35879	GCA_011801475.1	2371	2371	type	True	99.966	821	833	95	conclusive
Xylella fastidiosa	strain=DSM 10026	GCA_900129695.1	2371	2371	type	True	99.8504	761	833	95	conclusive
Xylella fastidiosa subsp. multiplex	strain=ATCC 35871	GCA_000428665.1	644357	2371	type	True	98.0041	748	833	95	conclusive
Xylella taiwanensis	strain=PLS229	GCA_013177435.1	1444770	1444770	type	True	82.6429	682	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:35:42,361] [INFO] DFAST Taxonomy check result was written to GCF_000767565.1_ASM76756v1_genomic.fna/tc_result.tsv
[2024-01-24 15:35:42,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:35:42,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:35:42,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/checkm_data
[2024-01-24 15:35:42,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:35:42,405] [INFO] Task started: CheckM
[2024-01-24 15:35:42,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000767565.1_ASM76756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000767565.1_ASM76756v1_genomic.fna/checkm_input GCF_000767565.1_ASM76756v1_genomic.fna/checkm_result
[2024-01-24 15:36:11,833] [INFO] Task succeeded: CheckM
[2024-01-24 15:36:11,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:36:11,854] [INFO] ===== Completeness check finished =====
[2024-01-24 15:36:11,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:36:11,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000767565.1_ASM76756v1_genomic.fna/markers.fasta)
[2024-01-24 15:36:11,856] [INFO] Task started: Blastn
[2024-01-24 15:36:11,856] [INFO] Running command: blastn -query GCF_000767565.1_ASM76756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1080b36-767e-49da-afb3-5a29250ea152/dqc_reference/reference_markers_gtdb.fasta -out GCF_000767565.1_ASM76756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:36:12,946] [INFO] Task succeeded: Blastn
[2024-01-24 15:36:12,950] [INFO] Selected 23 target genomes.
[2024-01-24 15:36:12,951] [INFO] Target genome list was writen to GCF_000767565.1_ASM76756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:36:12,984] [INFO] Task started: fastANI
[2024-01-24 15:36:12,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg606b4951-81bf-4d81-be20-335aa274384c/GCF_000767565.1_ASM76756v1_genomic.fna.gz --refList GCF_000767565.1_ASM76756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000767565.1_ASM76756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:36:28,579] [INFO] Task succeeded: fastANI
[2024-01-24 15:36:28,595] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:36:28,596] [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_011801475.1	s__Xylella fastidiosa	99.9663	821	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	98.40	96.23	0.96	0.89	130	conclusive
GCF_013177435.1	s__Xylella taiwanensis	82.659	676	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella	95.0	100.00	99.99	1.00	0.99	4	-
GCF_000007145.1	s__Xanthomonas campestris	76.9689	59	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.22	96.56	0.94	0.87	68	-
GCF_900183975.1	s__Xanthomonas fragariae	76.9554	57	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.74	99.53	0.99	0.96	62	-
GCF_001908725.1	s__Xanthomonas vesicatoria	76.7464	64	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_013387485.1	s__Stenotrophomonas maltophilia_AA	76.6659	53	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.19	96.54	0.90	0.89	3	-
GCF_001431465.1	s__Stenotrophomonas terrae	76.5827	55	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423585.1	s__Xanthomonas sp001423585	76.5406	68	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_002939865.1	s__Xanthomonas dyei	76.4547	62	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940205.1	s__Xanthomonas arboricola_C	76.3837	57	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:36:28,597] [INFO] GTDB search result was written to GCF_000767565.1_ASM76756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:36:28,598] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:36:28,601] [INFO] DFAST_QC result json was written to GCF_000767565.1_ASM76756v1_genomic.fna/dqc_result.json
[2024-01-24 15:36:28,602] [INFO] DFAST_QC completed!
[2024-01-24 15:36:28,602] [INFO] Total running time: 0h1m5s