[2024-01-24 13:12:38,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,865] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference
[2024-01-24 13:12:40,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,231] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e67041f-d28a-4810-a47d-a3eacb544990/GCF_002939885.1_ASM293988v1_genomic.fna.gz | prodigal -d GCF_002939885.1_ASM293988v1_genomic.fna/cds.fna -a GCF_002939885.1_ASM293988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:56,893] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:56,894] [INFO] Task started: HMMsearch
[2024-01-24 13:12:56,894] [INFO] Running command: hmmsearch --tblout GCF_002939885.1_ASM293988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/reference_markers.hmm GCF_002939885.1_ASM293988v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:57,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:57,200] [INFO] Found 6/6 markers.
[2024-01-24 13:12:57,237] [INFO] Query marker FASTA was written to GCF_002939885.1_ASM293988v1_genomic.fna/markers.fasta
[2024-01-24 13:12:57,238] [INFO] Task started: Blastn
[2024-01-24 13:12:57,238] [INFO] Running command: blastn -query GCF_002939885.1_ASM293988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/reference_markers.fasta -out GCF_002939885.1_ASM293988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:58,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:58,228] [INFO] Selected 16 target genomes.
[2024-01-24 13:12:58,229] [INFO] Target genome list was writen to GCF_002939885.1_ASM293988v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:58,238] [INFO] Task started: fastANI
[2024-01-24 13:12:58,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e67041f-d28a-4810-a47d-a3eacb544990/GCF_002939885.1_ASM293988v1_genomic.fna.gz --refList GCF_002939885.1_ASM293988v1_genomic.fna/target_genomes.txt --output GCF_002939885.1_ASM293988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:17,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:17,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:17,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:17,016] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:17,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:17,017] [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 cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	100.0	1401	1406	95	conclusive
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	89.9896	1192	1406	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	89.9022	1175	1406	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	89.8263	1216	1406	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	88.2938	1201	1406	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	87.1132	930	1406	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	86.5061	1128	1406	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	86.4428	1178	1406	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	86.4424	1055	1406	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 1833	GCA_017746675.1	1985254	1985254	pathovar	True	86.4397	1179	1406	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.4177	1137	1406	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.4108	1161	1406	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.3698	1155	1406	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	86.2849	1169	1406	95	below_threshold
Xanthomonas oryzae	strain=ATCC 35933	GCA_000482445.1	347	347	type	True	85.689	994	1406	95	below_threshold
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	85.4731	1057	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:17,019] [INFO] DFAST Taxonomy check result was written to GCF_002939885.1_ASM293988v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:17,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:17,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:17,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/checkm_data
[2024-01-24 13:13:17,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:17,066] [INFO] Task started: CheckM
[2024-01-24 13:13:17,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939885.1_ASM293988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939885.1_ASM293988v1_genomic.fna/checkm_input GCF_002939885.1_ASM293988v1_genomic.fna/checkm_result
[2024-01-24 13:14:10,179] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:10,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:10,206] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:10,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:10,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939885.1_ASM293988v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:10,208] [INFO] Task started: Blastn
[2024-01-24 13:14:10,208] [INFO] Running command: blastn -query GCF_002939885.1_ASM293988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54557202-e0bb-400c-8f02-7872ea9cd207/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939885.1_ASM293988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:11,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:11,970] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:11,970] [INFO] Target genome list was writen to GCF_002939885.1_ASM293988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:11,978] [INFO] Task started: fastANI
[2024-01-24 13:14:11,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e67041f-d28a-4810-a47d-a3eacb544990/GCF_002939885.1_ASM293988v1_genomic.fna.gz --refList GCF_002939885.1_ASM293988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939885.1_ASM293988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:24,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:24,474] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:24,474] [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_002939885.1	s__Xanthomonas cucurbitae	100.0	1401	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	conclusive
GCF_012848175.1	s__Xanthomonas campestris_C	90.2008	1222	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939785.1	s__Xanthomonas codiaei	89.9899	1200	1406	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	89.9766	1194	1406	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	89.8312	1215	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940015.1	s__Xanthomonas melonis	88.2748	1204	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802365.1	s__Xanthomonas cannabis	87.6304	1100	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_001010415.1	s__Xanthomonas pisi	87.0679	933	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003999565.1	s__Xanthomonas phaseoli	86.4661	1181	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_004136375.1	s__Xanthomonas oryzae	85.4757	1057	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:24,476] [INFO] GTDB search result was written to GCF_002939885.1_ASM293988v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:24,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:24,480] [INFO] DFAST_QC result json was written to GCF_002939885.1_ASM293988v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:24,480] [INFO] DFAST_QC completed!
[2024-01-24 13:14:24,480] [INFO] Total running time: 0h1m46s