[2023-06-26 23:45:11,926] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:45:11,928] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:45:11,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference
[2023-06-26 23:45:13,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:45:13,223] [INFO] Task started: Prodigal
[2023-06-26 23:45:13,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6c99fd1-3167-45e8-b8f0-e16f9b0d15a0/GCA_002430065.1_ASM243006v1_genomic.fna.gz | prodigal -d GCA_002430065.1_ASM243006v1_genomic.fna/cds.fna -a GCA_002430065.1_ASM243006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:45:19,460] [INFO] Task succeeded: Prodigal
[2023-06-26 23:45:19,461] [INFO] Task started: HMMsearch
[2023-06-26 23:45:19,461] [INFO] Running command: hmmsearch --tblout GCA_002430065.1_ASM243006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/reference_markers.hmm GCA_002430065.1_ASM243006v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:45:19,667] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:45:19,669] [INFO] Found 6/6 markers.
[2023-06-26 23:45:19,755] [INFO] Query marker FASTA was written to GCA_002430065.1_ASM243006v1_genomic.fna/markers.fasta
[2023-06-26 23:45:19,756] [INFO] Task started: Blastn
[2023-06-26 23:45:19,756] [INFO] Running command: blastn -query GCA_002430065.1_ASM243006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/reference_markers.fasta -out GCA_002430065.1_ASM243006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:45:20,371] [INFO] Task succeeded: Blastn
[2023-06-26 23:45:20,376] [INFO] Selected 25 target genomes.
[2023-06-26 23:45:20,377] [INFO] Target genome list was writen to GCA_002430065.1_ASM243006v1_genomic.fna/target_genomes.txt
[2023-06-26 23:45:20,391] [INFO] Task started: fastANI
[2023-06-26 23:45:20,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6c99fd1-3167-45e8-b8f0-e16f9b0d15a0/GCA_002430065.1_ASM243006v1_genomic.fna.gz --refList GCA_002430065.1_ASM243006v1_genomic.fna/target_genomes.txt --output GCA_002430065.1_ASM243006v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:45:36,857] [INFO] Task succeeded: fastANI
[2023-06-26 23:45:36,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:45:36,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:45:36,878] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:45:36,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:45:36,878] [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
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	76.5692	56	621	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.5615	68	621	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	76.5168	52	621	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	76.4972	86	621	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.4962	69	621	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.4367	92	621	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.3121	50	621	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	76.2673	63	621	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	76.2258	65	621	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	75.93	51	621	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	75.8718	52	621	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	75.8639	62	621	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	75.8603	60	621	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	75.8388	51	621	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	75.7977	56	621	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	75.7129	74	621	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:45:36,882] [INFO] DFAST Taxonomy check result was written to GCA_002430065.1_ASM243006v1_genomic.fna/tc_result.tsv
[2023-06-26 23:45:36,882] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:45:36,882] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:45:36,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/checkm_data
[2023-06-26 23:45:36,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:45:36,914] [INFO] Task started: CheckM
[2023-06-26 23:45:36,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002430065.1_ASM243006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002430065.1_ASM243006v1_genomic.fna/checkm_input GCA_002430065.1_ASM243006v1_genomic.fna/checkm_result
[2023-06-26 23:46:00,859] [INFO] Task succeeded: CheckM
[2023-06-26 23:46:00,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:46:00,885] [INFO] ===== Completeness check finished =====
[2023-06-26 23:46:00,885] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:46:00,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002430065.1_ASM243006v1_genomic.fna/markers.fasta)
[2023-06-26 23:46:00,886] [INFO] Task started: Blastn
[2023-06-26 23:46:00,886] [INFO] Running command: blastn -query GCA_002430065.1_ASM243006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg805b47cc-f2b2-428e-84fb-d01fc2f72b84/dqc_reference/reference_markers_gtdb.fasta -out GCA_002430065.1_ASM243006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:46:01,775] [INFO] Task succeeded: Blastn
[2023-06-26 23:46:01,780] [INFO] Selected 25 target genomes.
[2023-06-26 23:46:01,780] [INFO] Target genome list was writen to GCA_002430065.1_ASM243006v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:46:01,825] [INFO] Task started: fastANI
[2023-06-26 23:46:01,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6c99fd1-3167-45e8-b8f0-e16f9b0d15a0/GCA_002430065.1_ASM243006v1_genomic.fna.gz --refList GCA_002430065.1_ASM243006v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002430065.1_ASM243006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:46:17,602] [INFO] Task succeeded: fastANI
[2023-06-26 23:46:17,624] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:46:17,624] [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
GCA_018607835.1	s__RS62 sp002340675	98.9646	544	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	99.19	98.96	0.91	0.88	5	conclusive
GCA_000496475.1	s__RS62 sp000496475	78.4648	103	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	98.53	98.53	0.95	0.95	2	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	76.9339	82	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	76.8903	72	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269345.1	s__Limnohabitans_A sp001269345	76.7518	79	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256145.1	s__Limnohabitans_A sp002256145	76.7307	88	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.7227	63	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_017798165.1	s__Rhodoferax sp017798165	76.6986	53	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571145.1	s__Hydrogenophaga flava	76.5692	56	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063475.1	s__Limnohabitans curvus	76.4972	86	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	76.455	75	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175235.1	s__Acidovorax delafieldii_B	76.4256	61	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778325.1	s__Limnohabitans sp002778325	76.3405	91	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	76.3102	70	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	76.0779	60	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_016806145.1	s__Variovorax sp900115375	76.0484	64	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCA_001795455.1	s__Rhodoferax sp001795455	76.0377	65	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_003053545.1	s__Acidovorax sp003053545	76.0101	65	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_012932145.1	s__Giesbergeria sp012932145	75.9593	61	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_016721925.1	s__JAABQG01 sp016721925	75.9204	60	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_903902035.1	s__Curvibacter sp903902035	75.8496	52	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	98.85	97.80	0.89	0.83	3	-
GCF_014170375.1	s__Variovorax sp014170375	75.8418	72	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:46:17,626] [INFO] GTDB search result was written to GCA_002430065.1_ASM243006v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:46:17,626] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:46:17,631] [INFO] DFAST_QC result json was written to GCA_002430065.1_ASM243006v1_genomic.fna/dqc_result.json
[2023-06-26 23:46:17,631] [INFO] DFAST_QC completed!
[2023-06-26 23:46:17,631] [INFO] Total running time: 0h1m6s