[2024-01-24 11:51:11,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference
[2024-01-24 11:51:12,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,715] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e3a706-d8fd-4621-b716-244e392f8da5/GCF_004803715.2_ASM480371v2_genomic.fna.gz | prodigal -d GCF_004803715.2_ASM480371v2_genomic.fna/cds.fna -a GCF_004803715.2_ASM480371v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:23,028] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:23,029] [INFO] Task started: HMMsearch
[2024-01-24 11:51:23,029] [INFO] Running command: hmmsearch --tblout GCF_004803715.2_ASM480371v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/reference_markers.hmm GCF_004803715.2_ASM480371v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:23,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:23,299] [INFO] Found 6/6 markers.
[2024-01-24 11:51:23,327] [INFO] Query marker FASTA was written to GCF_004803715.2_ASM480371v2_genomic.fna/markers.fasta
[2024-01-24 11:51:23,328] [INFO] Task started: Blastn
[2024-01-24 11:51:23,328] [INFO] Running command: blastn -query GCF_004803715.2_ASM480371v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/reference_markers.fasta -out GCF_004803715.2_ASM480371v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:24,380] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:24,384] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:24,384] [INFO] Target genome list was writen to GCF_004803715.2_ASM480371v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:24,389] [INFO] Task started: fastANI
[2024-01-24 11:51:24,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e3a706-d8fd-4621-b716-244e392f8da5/GCF_004803715.2_ASM480371v2_genomic.fna.gz --refList GCF_004803715.2_ASM480371v2_genomic.fna/target_genomes.txt --output GCF_004803715.2_ASM480371v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:35,896] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:35,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:35,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:35,909] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:35,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:35,909] [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
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	100.0	1012	1013	95	conclusive
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	84.2901	739	1013	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	83.0768	741	1013	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	82.4016	635	1013	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	82.2514	645	1013	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	82.1546	691	1013	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.7245	596	1013	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.7215	505	1013	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.6833	661	1013	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.429	524	1013	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.421	555	1013	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	80.7781	537	1013	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	80.582	628	1013	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.012	601	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:35,911] [INFO] DFAST Taxonomy check result was written to GCF_004803715.2_ASM480371v2_genomic.fna/tc_result.tsv
[2024-01-24 11:51:35,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:35,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:35,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/checkm_data
[2024-01-24 11:51:35,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:35,943] [INFO] Task started: CheckM
[2024-01-24 11:51:35,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004803715.2_ASM480371v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004803715.2_ASM480371v2_genomic.fna/checkm_input GCF_004803715.2_ASM480371v2_genomic.fna/checkm_result
[2024-01-24 11:52:27,289] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:27,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:27,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:27,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004803715.2_ASM480371v2_genomic.fna/markers.fasta)
[2024-01-24 11:52:27,317] [INFO] Task started: Blastn
[2024-01-24 11:52:27,317] [INFO] Running command: blastn -query GCF_004803715.2_ASM480371v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dd77196-156a-47ce-84b5-431237f8805c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004803715.2_ASM480371v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:29,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:29,304] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:29,304] [INFO] Target genome list was writen to GCF_004803715.2_ASM480371v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:29,310] [INFO] Task started: fastANI
[2024-01-24 11:52:29,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e3a706-d8fd-4621-b716-244e392f8da5/GCF_004803715.2_ASM480371v2_genomic.fna.gz --refList GCF_004803715.2_ASM480371v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004803715.2_ASM480371v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:35,615] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,623] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:35,623] [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_004803715.2	s__Luteimonas yindakuii	100.0	1013	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.11	98.11	0.97	0.97	2	conclusive
GCF_004118975.1	s__Luteimonas sp004118975	89.1675	898	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002798175.1	s__Luteimonas sp002798175	88.7446	875	1013	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	84.3164	737	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482195.1	s__Luteimonas abyssi	83.0891	740	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	81.7854	685	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	81.0853	531	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,624] [INFO] GTDB search result was written to GCF_004803715.2_ASM480371v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:35,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:35,631] [INFO] DFAST_QC result json was written to GCF_004803715.2_ASM480371v2_genomic.fna/dqc_result.json
[2024-01-24 11:52:35,631] [INFO] DFAST_QC completed!
[2024-01-24 11:52:35,631] [INFO] Total running time: 0h1m24s