[2024-01-24 13:55:14,860] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference
[2024-01-24 13:55:16,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,228] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg80b37606-783a-4d3e-9980-10446a3bbb3d/GCF_000015565.1_ASM1556v1_genomic.fna.gz | prodigal -d GCF_000015565.1_ASM1556v1_genomic.fna/cds.fna -a GCF_000015565.1_ASM1556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:36,533] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:36,534] [INFO] Task started: HMMsearch
[2024-01-24 13:55:36,534] [INFO] Running command: hmmsearch --tblout GCF_000015565.1_ASM1556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/reference_markers.hmm GCF_000015565.1_ASM1556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:36,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:36,865] [INFO] Found 6/6 markers.
[2024-01-24 13:55:36,911] [INFO] Query marker FASTA was written to GCF_000015565.1_ASM1556v1_genomic.fna/markers.fasta
[2024-01-24 13:55:36,912] [INFO] Task started: Blastn
[2024-01-24 13:55:36,912] [INFO] Running command: blastn -query GCF_000015565.1_ASM1556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/reference_markers.fasta -out GCF_000015565.1_ASM1556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:37,899] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:37,903] [INFO] Selected 13 target genomes.
[2024-01-24 13:55:37,904] [INFO] Target genome list was writen to GCF_000015565.1_ASM1556v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:37,914] [INFO] Task started: fastANI
[2024-01-24 13:55:37,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg80b37606-783a-4d3e-9980-10446a3bbb3d/GCF_000015565.1_ASM1556v1_genomic.fna.gz --refList GCF_000015565.1_ASM1556v1_genomic.fna/target_genomes.txt --output GCF_000015565.1_ASM1556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:55,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:55,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:55,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:55,530] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:55,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:55,530] [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
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	100.0	1864	1865	95	conclusive
Verminephrobacter aporrectodeae subsp. tuberculatae	strain=At4	GCA_000193225.2	1110392	1110389	type	True	82.3223	714	1865	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	81.4962	748	1865	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	81.2062	721	1865	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	81.1217	758	1865	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	81.0615	629	1865	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.9898	737	1865	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.9293	589	1865	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	79.4509	541	1865	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1225	557	1865	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.0226	492	1865	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6937	544	1865	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.4104	594	1865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:55,532] [INFO] DFAST Taxonomy check result was written to GCF_000015565.1_ASM1556v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:55,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:55,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:55,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/checkm_data
[2024-01-24 13:55:55,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:55,588] [INFO] Task started: CheckM
[2024-01-24 13:55:55,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015565.1_ASM1556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015565.1_ASM1556v1_genomic.fna/checkm_input GCF_000015565.1_ASM1556v1_genomic.fna/checkm_result
[2024-01-24 13:58:11,047] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:11,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,071] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:11,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:11,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015565.1_ASM1556v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:11,073] [INFO] Task started: Blastn
[2024-01-24 13:58:11,073] [INFO] Running command: blastn -query GCF_000015565.1_ASM1556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6951d42a-904f-4cca-977f-3470025c849d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015565.1_ASM1556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,235] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:13,235] [INFO] Target genome list was writen to GCF_000015565.1_ASM1556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:13,268] [INFO] Task started: fastANI
[2024-01-24 13:58:13,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg80b37606-783a-4d3e-9980-10446a3bbb3d/GCF_000015565.1_ASM1556v1_genomic.fna.gz --refList GCF_000015565.1_ASM1556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015565.1_ASM1556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:41,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:41,670] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:41,670] [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_000015565.1	s__Acidovorax eiseniae	100.0	1864	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000193225.1	s__Acidovorax aporrectodeae	82.3307	712	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852545.1	s__Acidovorax sp003852545	81.906	749	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	81.784	790	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_001633105.1	s__Acidovorax sp001633105	81.6058	769	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424425.1	s__Acidovorax sp001424425	81.566	774	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_001422735.1	s__Acidovorax sp001422735	81.5554	747	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245625.1	s__Acidovorax kalamii	81.4918	747	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058055.1	s__Acidovorax sp003058055	81.4065	734	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_013376875.1	s__Acidovorax sp001411535	81.2675	752	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	-
GCF_003053545.1	s__Acidovorax sp003053545	81.213	795	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_003208485.1	s__Acidovorax sp003208485	81.1751	757	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	81.175	804	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408765.1	s__Acidovorax sp013408765	81.1498	773	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238595.1	s__Acidovorax facilis	81.1452	677	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCF_019219095.1	s__Acidovorax sp019219095	81.0934	763	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107605.1	s__Acidovorax soli	81.0574	630	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCA_011620245.1	s__Acidovorax sp011620245	80.8429	346	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210805.1	s__Acidovorax sp004210805	80.7466	607	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175235.1	s__Acidovorax delafieldii_B	80.5729	546	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102625.1	s__Acidovorax_A valerianellae	79.9379	586	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,672] [INFO] GTDB search result was written to GCF_000015565.1_ASM1556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:41,673] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:41,677] [INFO] DFAST_QC result json was written to GCF_000015565.1_ASM1556v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:41,677] [INFO] DFAST_QC completed!
[2024-01-24 13:58:41,677] [INFO] Total running time: 0h3m27s