[2024-01-25 20:16:50,600] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:50,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:50,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference
[2024-01-25 20:16:51,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:51,740] [INFO] Task started: Prodigal
[2024-01-25 20:16:51,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg355bd664-0932-4719-8033-687d8233a6e7/GCF_009674485.1_ASM967448v1_genomic.fna.gz | prodigal -d GCF_009674485.1_ASM967448v1_genomic.fna/cds.fna -a GCF_009674485.1_ASM967448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:20,224] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:20,224] [INFO] Task started: HMMsearch
[2024-01-25 20:17:20,224] [INFO] Running command: hmmsearch --tblout GCF_009674485.1_ASM967448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/reference_markers.hmm GCF_009674485.1_ASM967448v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:20,610] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:20,613] [INFO] Found 6/6 markers.
[2024-01-25 20:17:20,677] [INFO] Query marker FASTA was written to GCF_009674485.1_ASM967448v1_genomic.fna/markers.fasta
[2024-01-25 20:17:20,678] [INFO] Task started: Blastn
[2024-01-25 20:17:20,678] [INFO] Running command: blastn -query GCF_009674485.1_ASM967448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/reference_markers.fasta -out GCF_009674485.1_ASM967448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:21,455] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:21,458] [INFO] Selected 20 target genomes.
[2024-01-25 20:17:21,459] [INFO] Target genome list was writen to GCF_009674485.1_ASM967448v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:21,469] [INFO] Task started: fastANI
[2024-01-25 20:17:21,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg355bd664-0932-4719-8033-687d8233a6e7/GCF_009674485.1_ASM967448v1_genomic.fna.gz --refList GCF_009674485.1_ASM967448v1_genomic.fna/target_genomes.txt --output GCF_009674485.1_ASM967448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:48,984] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:48,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:48,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:48,997] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:48,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:48,997] [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
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	100.0	2682	2686	95	conclusive
Pseudoduganella ginsengisoli	strain=KCTC 42409	GCA_009720865.1	1462440	1462440	type	True	86.9245	1791	2686	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	82.2324	1617	2686	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	82.1023	1301	2686	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	81.064	1074	2686	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	80.9773	1104	2686	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	80.9701	1084	2686	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	80.8473	1142	2686	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	80.784	1038	2686	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.5051	1083	2686	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	80.4526	1058	2686	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	80.2209	991	2686	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	80.1094	1014	2686	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	80.0091	1110	2686	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	79.9896	980	2686	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	75.1291	61	2686	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.9742	159	2686	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	74.9727	54	2686	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	74.813	62	2686	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	74.6264	140	2686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:49,002] [INFO] DFAST Taxonomy check result was written to GCF_009674485.1_ASM967448v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:49,004] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:49,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:49,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/checkm_data
[2024-01-25 20:17:49,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:49,097] [INFO] Task started: CheckM
[2024-01-25 20:17:49,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674485.1_ASM967448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674485.1_ASM967448v1_genomic.fna/checkm_input GCF_009674485.1_ASM967448v1_genomic.fna/checkm_result
[2024-01-25 20:19:21,195] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:21,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:21,222] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:21,222] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:21,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674485.1_ASM967448v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:21,224] [INFO] Task started: Blastn
[2024-01-25 20:19:21,224] [INFO] Running command: blastn -query GCF_009674485.1_ASM967448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5756c472-1060-4223-bb5a-4ef4fc82f931/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674485.1_ASM967448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:22,604] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:22,607] [INFO] Selected 16 target genomes.
[2024-01-25 20:19:22,607] [INFO] Target genome list was writen to GCF_009674485.1_ASM967448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:22,624] [INFO] Task started: fastANI
[2024-01-25 20:19:22,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg355bd664-0932-4719-8033-687d8233a6e7/GCF_009674485.1_ASM967448v1_genomic.fna.gz --refList GCF_009674485.1_ASM967448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674485.1_ASM967448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:48,024] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:48,036] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:48,036] [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_009674485.1	s__Pseudoduganella sp009674485	100.0	2682	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009720865.1	s__Pseudoduganella ginsengisoli	86.931	1790	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116645.1	s__Pseudoduganella namucuonensis	82.238	1615	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053665.1	s__Pseudoduganella sp003053665	82.1776	1442	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.77	95.97	0.96	0.89	5	-
GCF_009857595.1	s__Pseudoduganella aquatica_A	82.0474	1312	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425265.1	s__Pseudoduganella sp001425265	81.9518	1423	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	81.9301	1453	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001191005.1	s__Pseudoduganella sp001191005	80.7789	1047	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008011715.1	s__Pseudoduganella haloabium	80.549	1060	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_009720835.1	s__Pseudoduganella buxea	80.4725	1055	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_019219065.1	s__Duganella sp019219065	80.2841	976	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143065.1	s__Duganella sacchari	80.1079	1013	2686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.30	97.30	0.91	0.91	2	-
GCF_003311635.1	s__Komagataeibacter cocois	74.9773	53	2686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	74.9725	154	2686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_015709455.1	s__Methylosinus sp015709455	74.9473	72	2686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899205.1	s__Mesorhizobium sp001899205	74.8635	152	2686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.31	96.64	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:48,040] [INFO] GTDB search result was written to GCF_009674485.1_ASM967448v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:48,041] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:48,047] [INFO] DFAST_QC result json was written to GCF_009674485.1_ASM967448v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:48,048] [INFO] DFAST_QC completed!
[2024-01-25 20:19:48,048] [INFO] Total running time: 0h2m57s