[2024-01-24 14:22:33,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference
[2024-01-24 14:22:34,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,820] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg49ac827e-f140-47e2-8d15-e36bace42445/GCF_002939865.1_ASM293986v1_genomic.fna.gz | prodigal -d GCF_002939865.1_ASM293986v1_genomic.fna/cds.fna -a GCF_002939865.1_ASM293986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:54,930] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:54,930] [INFO] Task started: HMMsearch
[2024-01-24 14:22:54,930] [INFO] Running command: hmmsearch --tblout GCF_002939865.1_ASM293986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/reference_markers.hmm GCF_002939865.1_ASM293986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:55,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:55,270] [INFO] Found 6/6 markers.
[2024-01-24 14:22:55,320] [INFO] Query marker FASTA was written to GCF_002939865.1_ASM293986v1_genomic.fna/markers.fasta
[2024-01-24 14:22:55,321] [INFO] Task started: Blastn
[2024-01-24 14:22:55,321] [INFO] Running command: blastn -query GCF_002939865.1_ASM293986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/reference_markers.fasta -out GCF_002939865.1_ASM293986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:56,241] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:56,244] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:56,245] [INFO] Target genome list was writen to GCF_002939865.1_ASM293986v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:56,255] [INFO] Task started: fastANI
[2024-01-24 14:22:56,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ac827e-f140-47e2-8d15-e36bace42445/GCF_002939865.1_ASM293986v1_genomic.fna.gz --refList GCF_002939865.1_ASM293986v1_genomic.fna/target_genomes.txt --output GCF_002939865.1_ASM293986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:17,144] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:17,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:17,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:17,163] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:17,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:17,163] [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 dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	100.0	1704	1706	95	conclusive
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	91.6636	1113	1706	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	91.1433	1450	1706	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	91.0508	1379	1706	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	88.5542	1422	1706	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	87.8801	1332	1706	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	87.6507	1333	1706	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	87.6397	1301	1706	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.455	1379	1706	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	87.3998	1365	1706	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	87.3636	1384	1706	95	below_threshold
Xanthomonas bromi	strain=CFBP1976	GCA_002939755.1	56449	56449	type	True	87.2194	1283	1706	95	below_threshold
Xanthomonas prunicola	strain=CFBP 8353	GCA_002846205.1	2053930	2053930	type	True	87.2141	1383	1706	95	below_threshold
Xanthomonas bromi		GCA_900092025.1	56449	56449	type	True	87.1549	1268	1706	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.7756	976	1706	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.4131	1074	1706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:17,171] [INFO] DFAST Taxonomy check result was written to GCF_002939865.1_ASM293986v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:17,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:17,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:17,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/checkm_data
[2024-01-24 14:23:17,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:17,286] [INFO] Task started: CheckM
[2024-01-24 14:23:17,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939865.1_ASM293986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939865.1_ASM293986v1_genomic.fna/checkm_input GCF_002939865.1_ASM293986v1_genomic.fna/checkm_result
[2024-01-24 14:24:18,426] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:18,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:18,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:18,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:18,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939865.1_ASM293986v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:18,451] [INFO] Task started: Blastn
[2024-01-24 14:24:18,451] [INFO] Running command: blastn -query GCF_002939865.1_ASM293986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b7c280-1d2c-4630-b458-85701d86483e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939865.1_ASM293986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:20,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:20,220] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:20,221] [INFO] Target genome list was writen to GCF_002939865.1_ASM293986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:20,231] [INFO] Task started: fastANI
[2024-01-24 14:24:20,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ac827e-f140-47e2-8d15-e36bace42445/GCF_002939865.1_ASM293986v1_genomic.fna.gz --refList GCF_002939865.1_ASM293986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939865.1_ASM293986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:38,599] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:38,613] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:38,613] [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_002939865.1	s__Xanthomonas dyei	100.0	1704	1706	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_001423585.1	s__Xanthomonas sp001423585	94.8272	1513	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_001010415.1	s__Xanthomonas pisi	91.6578	1113	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001908725.1	s__Xanthomonas vesicatoria	91.132	1451	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_001642575.1	s__Xanthomonas floridensis	88.5542	1422	1706	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	88.0989	1246	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_001660815.1	s__Xanthomonas nasturtii	87.8882	1331	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_012848175.1	s__Xanthomonas campestris_C	87.7856	1368	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423495.1	s__Xanthomonas sp001423495	87.3502	1378	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846205.1	s__Xanthomonas prunicola	87.2038	1384	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_900092025.1	s__Xanthomonas bromi	87.172	1267	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:38,615] [INFO] GTDB search result was written to GCF_002939865.1_ASM293986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:38,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:38,622] [INFO] DFAST_QC result json was written to GCF_002939865.1_ASM293986v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:38,623] [INFO] DFAST_QC completed!
[2024-01-24 14:24:38,623] [INFO] Total running time: 0h2m5s