[2024-01-24 13:47:11,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,347] [INFO] DQC Reference Directory: /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference
[2024-01-24 13:47:12,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,647] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgd444df43-ff18-4ac3-a221-2ce8190ac040/GCF_008033445.1_ASM803344v1_genomic.fna.gz | prodigal -d GCF_008033445.1_ASM803344v1_genomic.fna/cds.fna -a GCF_008033445.1_ASM803344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:20,845] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:20,846] [INFO] Task started: HMMsearch
[2024-01-24 13:47:20,846] [INFO] Running command: hmmsearch --tblout GCF_008033445.1_ASM803344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/reference_markers.hmm GCF_008033445.1_ASM803344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:21,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:21,076] [INFO] Found 6/6 markers.
[2024-01-24 13:47:21,108] [INFO] Query marker FASTA was written to GCF_008033445.1_ASM803344v1_genomic.fna/markers.fasta
[2024-01-24 13:47:21,108] [INFO] Task started: Blastn
[2024-01-24 13:47:21,109] [INFO] Running command: blastn -query GCF_008033445.1_ASM803344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/reference_markers.fasta -out GCF_008033445.1_ASM803344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:22,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:22,216] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:22,216] [INFO] Target genome list was writen to GCF_008033445.1_ASM803344v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:22,229] [INFO] Task started: fastANI
[2024-01-24 13:47:22,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgd444df43-ff18-4ac3-a221-2ce8190ac040/GCF_008033445.1_ASM803344v1_genomic.fna.gz --refList GCF_008033445.1_ASM803344v1_genomic.fna/target_genomes.txt --output GCF_008033445.1_ASM803344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:38,121] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:38,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:38,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:38,136] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:38,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:38,137] [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
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	100.0	865	866	95	conclusive
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	84.5784	595	866	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	84.4068	627	866	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	83.9379	592	866	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	83.8443	605	866	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	83.8286	624	866	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	83.4088	541	866	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	83.1628	552	866	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	83.0214	598	866	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.9141	589	866	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	82.8865	606	866	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	82.8751	518	866	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	82.7363	547	866	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	82.3413	559	866	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	82.3346	615	866	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	82.1502	586	866	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	82.1428	543	866	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.5189	585	866	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.3088	479	866	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.2934	560	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:38,139] [INFO] DFAST Taxonomy check result was written to GCF_008033445.1_ASM803344v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:38,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:38,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:38,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/checkm_data
[2024-01-24 13:47:38,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:38,168] [INFO] Task started: CheckM
[2024-01-24 13:47:38,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008033445.1_ASM803344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008033445.1_ASM803344v1_genomic.fna/checkm_input GCF_008033445.1_ASM803344v1_genomic.fna/checkm_result
[2024-01-24 13:48:20,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:20,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:20,094] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:20,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:20,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008033445.1_ASM803344v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:20,096] [INFO] Task started: Blastn
[2024-01-24 13:48:20,096] [INFO] Running command: blastn -query GCF_008033445.1_ASM803344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd66d3e7a-0d44-4b08-953a-c58547fb3add/dqc_reference/reference_markers_gtdb.fasta -out GCF_008033445.1_ASM803344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:22,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:22,207] [INFO] Selected 20 target genomes.
[2024-01-24 13:48:22,207] [INFO] Target genome list was writen to GCF_008033445.1_ASM803344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:22,230] [INFO] Task started: fastANI
[2024-01-24 13:48:22,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgd444df43-ff18-4ac3-a221-2ce8190ac040/GCF_008033445.1_ASM803344v1_genomic.fna.gz --refList GCF_008033445.1_ASM803344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008033445.1_ASM803344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:36,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:36,991] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:36,991] [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_008033445.1	s__Vulcaniibacterium_B gelatinicum	100.0	865	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003814555.1	s__Lysobacter tengchongensis	84.4503	624	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003416885.1	s__Luteimonas_B sp003416885	83.8996	594	866	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_007923255.1	s__Lysobacter thermophilus	83.8836	602	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	83.1892	550	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_007859325.1	s__Luteimonas marina	82.9533	603	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	82.8855	606	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	82.8801	589	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	82.7174	548	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	82.5547	572	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	82.4865	596	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	82.4697	454	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	82.3742	472	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	82.3315	615	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312895.1	s__Luteimonas sp008312895	82.2713	582	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	82.0121	540	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	81.8166	580	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	81.7008	504	866	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_016735495.2	s__Lysobacter sp016735495	81.5959	584	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	81.4206	543	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:36,993] [INFO] GTDB search result was written to GCF_008033445.1_ASM803344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:36,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:36,998] [INFO] DFAST_QC result json was written to GCF_008033445.1_ASM803344v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:36,998] [INFO] DFAST_QC completed!
[2024-01-24 13:48:36,998] [INFO] Total running time: 0h1m26s