[2024-01-24 10:47:06,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,821] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg354e5955-6b04-4a31-9f18-772ba6675e20/GCF_014236795.1_ASM1423679v1_genomic.fna.gz | prodigal -d GCF_014236795.1_ASM1423679v1_genomic.fna/cds.fna -a GCF_014236795.1_ASM1423679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:28,147] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:28,148] [INFO] Task started: HMMsearch
[2024-01-24 10:47:28,148] [INFO] Running command: hmmsearch --tblout GCF_014236795.1_ASM1423679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/reference_markers.hmm GCF_014236795.1_ASM1423679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:28,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:28,447] [INFO] Found 6/6 markers.
[2024-01-24 10:47:28,487] [INFO] Query marker FASTA was written to GCF_014236795.1_ASM1423679v1_genomic.fna/markers.fasta
[2024-01-24 10:47:28,488] [INFO] Task started: Blastn
[2024-01-24 10:47:28,488] [INFO] Running command: blastn -query GCF_014236795.1_ASM1423679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/reference_markers.fasta -out GCF_014236795.1_ASM1423679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:29,604] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:29,607] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:29,608] [INFO] Target genome list was writen to GCF_014236795.1_ASM1423679v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:30,046] [INFO] Task started: fastANI
[2024-01-24 10:47:30,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg354e5955-6b04-4a31-9f18-772ba6675e20/GCF_014236795.1_ASM1423679v1_genomic.fna.gz --refList GCF_014236795.1_ASM1423679v1_genomic.fna/target_genomes.txt --output GCF_014236795.1_ASM1423679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:48,784] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:48,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:48,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:48,796] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:48,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:48,797] [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 theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	100.0	1591	1594	95	conclusive
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	99.8491	1346	1594	95	conclusive
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	90.7091	1090	1594	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	90.5957	1095	1594	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	89.9911	909	1594	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	88.0403	1084	1594	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	82.8599	731	1594	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.5543	659	1594	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	81.9397	895	1594	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	81.5982	878	1594	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	81.5091	861	1594	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.1517	706	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:48,798] [INFO] DFAST Taxonomy check result was written to GCF_014236795.1_ASM1423679v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:48,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:48,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:48,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/checkm_data
[2024-01-24 10:47:48,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:48,853] [INFO] Task started: CheckM
[2024-01-24 10:47:48,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014236795.1_ASM1423679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014236795.1_ASM1423679v1_genomic.fna/checkm_input GCF_014236795.1_ASM1423679v1_genomic.fna/checkm_result
[2024-01-24 10:48:45,296] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:45,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,324] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:45,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:45,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014236795.1_ASM1423679v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:45,325] [INFO] Task started: Blastn
[2024-01-24 10:48:45,326] [INFO] Running command: blastn -query GCF_014236795.1_ASM1423679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5929dbbc-8485-49ca-aa11-03ad50cb12bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014236795.1_ASM1423679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:47,438] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:47,443] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:47,443] [INFO] Target genome list was writen to GCF_014236795.1_ASM1423679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:47,452] [INFO] Task started: fastANI
[2024-01-24 10:48:47,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg354e5955-6b04-4a31-9f18-772ba6675e20/GCF_014236795.1_ASM1423679v1_genomic.fna.gz --refList GCF_014236795.1_ASM1423679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014236795.1_ASM1423679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:04,247] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:04,262] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:04,262] [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_014236795.1	s__Xanthomonas_A theicola	100.0	1592	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_007829315.1	s__Xanthomonas_A translucens_A	91.4245	1142	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	90.6118	1093	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014236855.1	s__Xanthomonas_A sp014236855	90.4087	1141	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	90.1735	1115	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331775.1	s__Xanthomonas_A translucens	89.7041	888	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.09	95.18	0.88	0.77	59	-
GCF_017163755.1	s__Xanthomonas_A sp017163755	88.3324	1048	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	83.0285	759	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	82.8431	706	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCA_017745195.1	s__Pseudoxanthomonas sp017745195	81.8508	646	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	80.5979	707	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:04,264] [INFO] GTDB search result was written to GCF_014236795.1_ASM1423679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:04,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:04,268] [INFO] DFAST_QC result json was written to GCF_014236795.1_ASM1423679v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:04,268] [INFO] DFAST_QC completed!
[2024-01-24 10:49:04,269] [INFO] Total running time: 0h1m58s