[2024-01-24 12:22:14,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference
[2024-01-24 12:22:15,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,607] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg10b1ed54-8714-4b6a-9c71-1f5fc8071be5/GCF_001908725.1_ASM190872v1_genomic.fna.gz | prodigal -d GCF_001908725.1_ASM190872v1_genomic.fna/cds.fna -a GCF_001908725.1_ASM190872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:34,843] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:34,843] [INFO] Task started: HMMsearch
[2024-01-24 12:22:34,844] [INFO] Running command: hmmsearch --tblout GCF_001908725.1_ASM190872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/reference_markers.hmm GCF_001908725.1_ASM190872v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:35,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:35,230] [INFO] Found 6/6 markers.
[2024-01-24 12:22:35,282] [INFO] Query marker FASTA was written to GCF_001908725.1_ASM190872v1_genomic.fna/markers.fasta
[2024-01-24 12:22:35,283] [INFO] Task started: Blastn
[2024-01-24 12:22:35,283] [INFO] Running command: blastn -query GCF_001908725.1_ASM190872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/reference_markers.fasta -out GCF_001908725.1_ASM190872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:36,250] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:36,254] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:36,255] [INFO] Target genome list was writen to GCF_001908725.1_ASM190872v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:36,261] [INFO] Task started: fastANI
[2024-01-24 12:22:36,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b1ed54-8714-4b6a-9c71-1f5fc8071be5/GCF_001908725.1_ASM190872v1_genomic.fna.gz --refList GCF_001908725.1_ASM190872v1_genomic.fna/target_genomes.txt --output GCF_001908725.1_ASM190872v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:56,135] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:56,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:56,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:56,147] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:56,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:56,147] [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 vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	100.0	1782	1782	95	conclusive
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	99.8956	1651	1782	95	conclusive
Xanthomonas dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	91.0182	1459	1782	95	below_threshold
Xanthomonas pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	90.6182	1096	1782	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	88.5394	1419	1782	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	87.8798	1362	1782	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	87.7654	1337	1782	95	below_threshold
Xanthomonas bromi	strain=CFBP1976	GCA_002939755.1	56449	56449	type	True	87.2637	1279	1782	95	below_threshold
Xanthomonas bromi		GCA_900092025.1	56449	56449	type	True	87.2027	1269	1782	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.9649	1364	1782	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.9484	1362	1782	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.9299	1380	1782	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	86.6261	1383	1782	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	86.4293	1399	1782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:56,151] [INFO] DFAST Taxonomy check result was written to GCF_001908725.1_ASM190872v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:56,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:56,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:56,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/checkm_data
[2024-01-24 12:22:56,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:56,217] [INFO] Task started: CheckM
[2024-01-24 12:22:56,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001908725.1_ASM190872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001908725.1_ASM190872v1_genomic.fna/checkm_input GCF_001908725.1_ASM190872v1_genomic.fna/checkm_result
[2024-01-24 12:23:55,792] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:55,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,818] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:55,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:55,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001908725.1_ASM190872v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:55,819] [INFO] Task started: Blastn
[2024-01-24 12:23:55,819] [INFO] Running command: blastn -query GCF_001908725.1_ASM190872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268902bc-a34d-44ba-8f17-95033788aba1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001908725.1_ASM190872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:57,502] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:57,506] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:57,506] [INFO] Target genome list was writen to GCF_001908725.1_ASM190872v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:57,515] [INFO] Task started: fastANI
[2024-01-24 12:23:57,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b1ed54-8714-4b6a-9c71-1f5fc8071be5/GCF_001908725.1_ASM190872v1_genomic.fna.gz --refList GCF_001908725.1_ASM190872v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001908725.1_ASM190872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:12,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:12,237] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:12,237] [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_001908725.1	s__Xanthomonas vesicatoria	100.0	1782	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	conclusive
GCF_002939865.1	s__Xanthomonas dyei	91.0296	1458	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423585.1	s__Xanthomonas sp001423585	90.6742	1460	1782	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	90.606	1097	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001642575.1	s__Xanthomonas floridensis	88.5493	1418	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660815.1	s__Xanthomonas nasturtii	87.8813	1362	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_000802365.1	s__Xanthomonas cannabis	87.8771	1278	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_000454545.1	s__Xanthomonas cassavae	87.6832	1365	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092025.1	s__Xanthomonas bromi	87.1961	1270	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014197275.1	s__Xanthomonas campestris_B	87.0542	1300	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCF_002846205.1	s__Xanthomonas prunicola	86.8952	1368	1782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:12,239] [INFO] GTDB search result was written to GCF_001908725.1_ASM190872v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:12,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:12,244] [INFO] DFAST_QC result json was written to GCF_001908725.1_ASM190872v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:12,244] [INFO] DFAST_QC completed!
[2024-01-24 12:24:12,244] [INFO] Total running time: 0h1m58s