[2024-01-24 11:51:09,765] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:09,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:09,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference
[2024-01-24 11:51:11,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,089] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,089] [INFO] Running command: gunzip -c /var/lib/cwl/stg19645113-bd3a-4af7-8302-b1cb118d2a14/GCF_010093205.1_ASM1009320v1_genomic.fna.gz | prodigal -d GCF_010093205.1_ASM1009320v1_genomic.fna/cds.fna -a GCF_010093205.1_ASM1009320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:22,518] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:22,519] [INFO] Task started: HMMsearch
[2024-01-24 11:51:22,519] [INFO] Running command: hmmsearch --tblout GCF_010093205.1_ASM1009320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/reference_markers.hmm GCF_010093205.1_ASM1009320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:22,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:22,803] [INFO] Found 6/6 markers.
[2024-01-24 11:51:22,850] [INFO] Query marker FASTA was written to GCF_010093205.1_ASM1009320v1_genomic.fna/markers.fasta
[2024-01-24 11:51:22,851] [INFO] Task started: Blastn
[2024-01-24 11:51:22,851] [INFO] Running command: blastn -query GCF_010093205.1_ASM1009320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/reference_markers.fasta -out GCF_010093205.1_ASM1009320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:23,862] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:23,866] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:23,867] [INFO] Target genome list was writen to GCF_010093205.1_ASM1009320v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:23,873] [INFO] Task started: fastANI
[2024-01-24 11:51:23,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg19645113-bd3a-4af7-8302-b1cb118d2a14/GCF_010093205.1_ASM1009320v1_genomic.fna.gz --refList GCF_010093205.1_ASM1009320v1_genomic.fna/target_genomes.txt --output GCF_010093205.1_ASM1009320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,594] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,607] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:37,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:37,607] [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
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	100.0	1169	1173	95	conclusive
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	87.6023	949	1173	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	86.991	805	1173	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	86.1504	854	1173	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	85.1366	802	1173	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	85.1124	809	1173	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	84.7184	820	1173	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	82.3548	754	1173	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.3527	752	1173	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	82.3263	750	1173	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.1465	636	1173	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.9965	727	1173	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.3872	598	1173	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.1779	693	1173	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	80.7282	594	1173	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.7024	670	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,609] [INFO] DFAST Taxonomy check result was written to GCF_010093205.1_ASM1009320v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,610] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,610] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/checkm_data
[2024-01-24 11:51:37,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,650] [INFO] Task started: CheckM
[2024-01-24 11:51:37,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093205.1_ASM1009320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093205.1_ASM1009320v1_genomic.fna/checkm_input GCF_010093205.1_ASM1009320v1_genomic.fna/checkm_result
[2024-01-24 11:52:16,032] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:16,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,050] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:16,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:16,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093205.1_ASM1009320v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:16,051] [INFO] Task started: Blastn
[2024-01-24 11:52:16,051] [INFO] Running command: blastn -query GCF_010093205.1_ASM1009320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dcd1a7e-4d99-4ec2-9a87-19f7ffc0ebd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093205.1_ASM1009320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,857] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,861] [INFO] Selected 15 target genomes.
[2024-01-24 11:52:17,861] [INFO] Target genome list was writen to GCF_010093205.1_ASM1009320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:17,870] [INFO] Task started: fastANI
[2024-01-24 11:52:17,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg19645113-bd3a-4af7-8302-b1cb118d2a14/GCF_010093205.1_ASM1009320v1_genomic.fna.gz --refList GCF_010093205.1_ASM1009320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093205.1_ASM1009320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:30,773] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:30,786] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:30,786] [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_010093205.1	s__Pseudoxanthomonas daejeonensis	100.0	1169	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	87.5911	949	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	87.4937	943	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	87.0065	804	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745195.1	s__Pseudoxanthomonas sp017745195	86.8567	863	1173	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	86.3012	864	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	86.2043	864	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	86.1506	855	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302035.1	s__Pseudoxanthomonas sp017302035	85.3192	660	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	85.1083	805	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	82.5986	800	1173	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_017163755.1	s__Xanthomonas_A sp017163755	82.5949	796	1173	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	82.3339	756	1173	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_006476065.1	s__Luteimonas_B lumbrici	80.8696	504	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	80.8104	686	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:30,788] [INFO] GTDB search result was written to GCF_010093205.1_ASM1009320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:30,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:30,793] [INFO] DFAST_QC result json was written to GCF_010093205.1_ASM1009320v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:30,793] [INFO] DFAST_QC completed!
[2024-01-24 11:52:30,793] [INFO] Total running time: 0h1m21s