[2024-01-24 12:13:27,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,700] [INFO] DQC Reference Directory: /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference
[2024-01-24 12:13:28,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,998] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,998] [INFO] Running command: gunzip -c /var/lib/cwl/stg58ea3527-d23c-48cb-a61e-68e3131c46e1/GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/cds.fna -a GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:46,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:46,153] [INFO] Task started: HMMsearch
[2024-01-24 12:13:46,153] [INFO] Running command: hmmsearch --tblout GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/reference_markers.hmm GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:46,487] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:46,488] [INFO] Found 6/6 markers.
[2024-01-24 12:13:46,533] [INFO] Query marker FASTA was written to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:46,534] [INFO] Task started: Blastn
[2024-01-24 12:13:46,534] [INFO] Running command: blastn -query GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/reference_markers.fasta -out GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:47,650] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:47,653] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:47,654] [INFO] Target genome list was writen to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:47,664] [INFO] Task started: fastANI
[2024-01-24 12:13:47,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ea3527-d23c-48cb-a61e-68e3131c46e1/GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna.gz --refList GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,256] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,272] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:12,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:12,273] [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
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	100.0	1747	1749	95	conclusive
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	85.1017	1092	1749	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	84.993	1111	1749	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	84.8551	1103	1749	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	84.808	1042	1749	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	84.6284	1014	1749	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	84.0647	989	1749	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	83.7341	988	1749	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	82.1761	874	1749	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.0873	823	1749	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	82.0617	912	1749	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	82.0298	946	1749	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.8325	882	1749	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	81.8006	754	1749	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.3757	634	1749	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.3046	632	1749	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0744	719	1749	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.0701	705	1749	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.4695	754	1749	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	80.4296	707	1749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,278] [INFO] DFAST Taxonomy check result was written to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/checkm_data
[2024-01-24 12:14:12,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,330] [INFO] Task started: CheckM
[2024-01-24 12:14:12,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/checkm_input GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:15:16,408] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:16,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:16,435] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:16,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:16,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:15:16,436] [INFO] Task started: Blastn
[2024-01-24 12:15:16,436] [INFO] Running command: blastn -query GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge2b9770c-f3a8-413f-abfe-1594496fec47/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:18,938] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:18,942] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:18,942] [INFO] Target genome list was writen to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:18,975] [INFO] Task started: fastANI
[2024-01-24 12:15:18,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ea3527-d23c-48cb-a61e-68e3131c46e1/GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna.gz --refList GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:37,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:37,049] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:37,049] [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_900113035.1	s__Acidovorax_A wautersii	100.0	1747	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424265.1	s__Acidovorax_A sp001424265	87.3812	1140	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687165.1	s__Acidovorax_A oryzae	85.1214	1091	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_000176855.2	s__Acidovorax_A avenae	85.0445	1105	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCA_002397315.1	s__Acidovorax_A sp002397315	85.0424	1070	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	84.808	1042	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_003269065.1	s__Acidovorax_A anthurii	84.6269	1013	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400995.2	s__MR-S7 sp000400995	84.2749	910	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_900112675.1	s__Acidovorax_A konjaci	83.9901	997	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	83.9336	937	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_014207955.1	s__Acidovorax soli_A	83.2108	1028	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363755.1	s__Comamonas antarcticus	81.7816	782	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341365.1	s__Giesbergeria metamorpha	81.378	633	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,052] [INFO] GTDB search result was written to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:37,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:37,060] [INFO] DFAST_QC result json was written to GCF_900113035.1_IMG-taxon_2634166330_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:15:37,060] [INFO] DFAST_QC completed!
[2024-01-24 12:15:37,060] [INFO] Total running time: 0h2m9s