[2024-01-24 14:28:18,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference
[2024-01-24 14:28:20,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,483] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b60cb4e-91b2-4767-b8ce-fbb6e5914c56/GCF_020783655.1_ASM2078365v1_genomic.fna.gz | prodigal -d GCF_020783655.1_ASM2078365v1_genomic.fna/cds.fna -a GCF_020783655.1_ASM2078365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:37,289] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:37,289] [INFO] Task started: HMMsearch
[2024-01-24 14:28:37,289] [INFO] Running command: hmmsearch --tblout GCF_020783655.1_ASM2078365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/reference_markers.hmm GCF_020783655.1_ASM2078365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:37,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:37,605] [INFO] Found 6/6 markers.
[2024-01-24 14:28:37,677] [INFO] Query marker FASTA was written to GCF_020783655.1_ASM2078365v1_genomic.fna/markers.fasta
[2024-01-24 14:28:37,678] [INFO] Task started: Blastn
[2024-01-24 14:28:37,678] [INFO] Running command: blastn -query GCF_020783655.1_ASM2078365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/reference_markers.fasta -out GCF_020783655.1_ASM2078365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:38,772] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:38,780] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:38,781] [INFO] Target genome list was writen to GCF_020783655.1_ASM2078365v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:38,799] [INFO] Task started: fastANI
[2024-01-24 14:28:38,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b60cb4e-91b2-4767-b8ce-fbb6e5914c56/GCF_020783655.1_ASM2078365v1_genomic.fna.gz --refList GCF_020783655.1_ASM2078365v1_genomic.fna/target_genomes.txt --output GCF_020783655.1_ASM2078365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:59,304] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:59,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:59,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:59,318] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:59,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:59,318] [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
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	100.0	1537	1540	95	conclusive
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	88.3385	1264	1540	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	88.3195	1298	1540	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	88.2496	1342	1540	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	88.201	1196	1540	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	86.9571	1008	1540	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	86.6881	1238	1540	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	86.5176	1274	1540	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	86.4956	1280	1540	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	86.363	1235	1540	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	86.3452	1264	1540	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	86.333	1241	1540	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	86.2841	1285	1540	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.2559	1255	1540	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.0986	1244	1540	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.0322	1250	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:59,320] [INFO] DFAST Taxonomy check result was written to GCF_020783655.1_ASM2078365v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:59,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:59,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:59,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/checkm_data
[2024-01-24 14:28:59,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:59,373] [INFO] Task started: CheckM
[2024-01-24 14:28:59,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020783655.1_ASM2078365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020783655.1_ASM2078365v1_genomic.fna/checkm_input GCF_020783655.1_ASM2078365v1_genomic.fna/checkm_result
[2024-01-24 14:29:55,183] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:55,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:55,206] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:55,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:55,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020783655.1_ASM2078365v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:55,208] [INFO] Task started: Blastn
[2024-01-24 14:29:55,208] [INFO] Running command: blastn -query GCF_020783655.1_ASM2078365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf34376-d25c-4252-af6e-ec09125bbed1/dqc_reference/reference_markers_gtdb.fasta -out GCF_020783655.1_ASM2078365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:57,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:57,047] [INFO] Selected 10 target genomes.
[2024-01-24 14:29:57,047] [INFO] Target genome list was writen to GCF_020783655.1_ASM2078365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:57,055] [INFO] Task started: fastANI
[2024-01-24 14:29:57,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b60cb4e-91b2-4767-b8ce-fbb6e5914c56/GCF_020783655.1_ASM2078365v1_genomic.fna.gz --refList GCF_020783655.1_ASM2078365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020783655.1_ASM2078365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:10,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:10,085] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:10,085] [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_002940015.1	s__Xanthomonas melonis	99.996	1535	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002939785.1	s__Xanthomonas codiaei	88.7096	1352	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848175.1	s__Xanthomonas campestris_C	88.6199	1312	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454545.1	s__Xanthomonas cassavae	88.3107	1299	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642575.1	s__Xanthomonas floridensis	88.262	1341	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939885.1	s__Xanthomonas cucurbitae	88.201	1196	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_001660815.1	s__Xanthomonas nasturtii	86.6893	1238	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_013112235.1	s__Xanthomonas perforans	86.3616	1298	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_003999565.1	s__Xanthomonas phaseoli	86.3269	1277	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001304695.1	s__Xanthomonas axonopodis	85.8355	1076	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:10,088] [INFO] GTDB search result was written to GCF_020783655.1_ASM2078365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:10,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:10,094] [INFO] DFAST_QC result json was written to GCF_020783655.1_ASM2078365v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:10,094] [INFO] DFAST_QC completed!
[2024-01-24 14:30:10,094] [INFO] Total running time: 0h1m52s