[2024-01-24 14:14:06,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference
[2024-01-24 14:14:07,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,520] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg59e98f75-ba00-4854-bd67-27680cceaa29/GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/cds.fna -a GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:35,501] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:35,502] [INFO] Task started: HMMsearch
[2024-01-24 14:14:35,502] [INFO] Running command: hmmsearch --tblout GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/reference_markers.hmm GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:35,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:35,921] [INFO] Found 6/6 markers.
[2024-01-24 14:14:35,998] [INFO] Query marker FASTA was written to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:35,999] [INFO] Task started: Blastn
[2024-01-24 14:14:35,999] [INFO] Running command: blastn -query GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/reference_markers.fasta -out GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:37,202] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:37,206] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:37,207] [INFO] Target genome list was writen to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:37,238] [INFO] Task started: fastANI
[2024-01-24 14:14:37,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e98f75-ba00-4854-bd67-27680cceaa29/GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna.gz --refList GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:09,975] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:09,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:09,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:09,995] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:09,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:09,995] [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 namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	100.0	2767	2774	95	conclusive
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	85.8115	1494	2774	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	83.2311	1186	2774	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	83.2099	1249	2774	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.1	1337	2774	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.0787	1303	2774	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.9638	1219	2774	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	82.892	1346	2774	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	82.6303	1201	2774	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	82.5954	1260	2774	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.4622	1264	2774	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	82.3845	1178	2774	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	82.2624	1193	2774	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	82.2123	1627	2774	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	82.1494	1237	2774	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	81.5826	1180	2774	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.9641	1155	2774	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	80.911	977	2774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,997] [INFO] DFAST Taxonomy check result was written to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:09,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:09,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:09,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/checkm_data
[2024-01-24 14:15:09,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:10,080] [INFO] Task started: CheckM
[2024-01-24 14:15:10,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/checkm_input GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:16:34,237] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:34,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:34,265] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:34,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:34,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:16:34,267] [INFO] Task started: Blastn
[2024-01-24 14:16:34,267] [INFO] Running command: blastn -query GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2515bf17-6bd3-4d4d-ae71-33970b40dcc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:36,574] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:36,577] [INFO] Selected 7 target genomes.
[2024-01-24 14:16:36,577] [INFO] Target genome list was writen to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:36,582] [INFO] Task started: fastANI
[2024-01-24 14:16:36,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e98f75-ba00-4854-bd67-27680cceaa29/GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna.gz --refList GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:53,858] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:53,871] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:53,872] [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_900116645.1	s__Pseudoduganella namucuonensis	100.0	2767	2774	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_003053665.1	s__Pseudoduganella sp003053665	85.9673	1629	2774	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	85.7912	1498	2774	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	85.7247	1621	2774	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	85.7112	1663	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461825.1	s__Rugamonas sp016461825	83.4284	1323	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674485.1	s__Pseudoduganella sp009674485	82.1943	1632	2774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:53,873] [INFO] GTDB search result was written to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:53,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:53,879] [INFO] DFAST_QC result json was written to GCF_900116645.1_IMG-taxon_2671180040_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:16:53,879] [INFO] DFAST_QC completed!
[2024-01-24 14:16:53,879] [INFO] Total running time: 0h2m48s