[2024-01-24 12:13:50,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:50,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:50,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference
[2024-01-24 12:13:52,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:52,212] [INFO] Task started: Prodigal
[2024-01-24 12:13:52,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b38e951-00a8-4938-9ceb-f4f8c5c85dda/GCF_003337425.1_ASM333742v1_genomic.fna.gz | prodigal -d GCF_003337425.1_ASM333742v1_genomic.fna/cds.fna -a GCF_003337425.1_ASM333742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:02,940] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:02,940] [INFO] Task started: HMMsearch
[2024-01-24 12:14:02,940] [INFO] Running command: hmmsearch --tblout GCF_003337425.1_ASM333742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/reference_markers.hmm GCF_003337425.1_ASM333742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:03,214] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:03,216] [INFO] Found 6/6 markers.
[2024-01-24 12:14:03,244] [INFO] Query marker FASTA was written to GCF_003337425.1_ASM333742v1_genomic.fna/markers.fasta
[2024-01-24 12:14:03,245] [INFO] Task started: Blastn
[2024-01-24 12:14:03,245] [INFO] Running command: blastn -query GCF_003337425.1_ASM333742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/reference_markers.fasta -out GCF_003337425.1_ASM333742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:04,232] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:04,235] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:04,236] [INFO] Target genome list was writen to GCF_003337425.1_ASM333742v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:04,259] [INFO] Task started: fastANI
[2024-01-24 12:14:04,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b38e951-00a8-4938-9ceb-f4f8c5c85dda/GCF_003337425.1_ASM333742v1_genomic.fna.gz --refList GCF_003337425.1_ASM333742v1_genomic.fna/target_genomes.txt --output GCF_003337425.1_ASM333742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:19,227] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:19,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:19,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:19,240] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:14:19,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:19,240] [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
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	100.0	1016	1017	95	conclusive
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	99.986	1008	1017	95	conclusive
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	99.9804	1006	1017	95	conclusive
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	91.3706	819	1017	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.5901	590	1017	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.1419	509	1017	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	79.8438	558	1017	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.5184	518	1017	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.4627	470	1017	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.4579	502	1017	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	79.3315	475	1017	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.3208	475	1017	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.8927	462	1017	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.1344	360	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:19,242] [INFO] DFAST Taxonomy check result was written to GCF_003337425.1_ASM333742v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:19,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:19,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:19,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/checkm_data
[2024-01-24 12:14:19,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:19,276] [INFO] Task started: CheckM
[2024-01-24 12:14:19,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337425.1_ASM333742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337425.1_ASM333742v1_genomic.fna/checkm_input GCF_003337425.1_ASM333742v1_genomic.fna/checkm_result
[2024-01-24 12:14:56,004] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:56,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,027] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:56,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:56,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337425.1_ASM333742v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:56,029] [INFO] Task started: Blastn
[2024-01-24 12:14:56,029] [INFO] Running command: blastn -query GCF_003337425.1_ASM333742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d911b8-c895-4720-a67f-9ad8898025da/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337425.1_ASM333742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:58,046] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:58,052] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:58,052] [INFO] Target genome list was writen to GCF_003337425.1_ASM333742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:58,073] [INFO] Task started: fastANI
[2024-01-24 12:14:58,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b38e951-00a8-4938-9ceb-f4f8c5c85dda/GCF_003337425.1_ASM333742v1_genomic.fna.gz --refList GCF_003337425.1_ASM333742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337425.1_ASM333742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:15,722] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,743] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:15,743] [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_003337425.1	s__Extensimonas vulgaris	100.0	1016	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_007655255.1	s__Extensimonas perlucida	91.3435	821	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	97.84	97.67	0.89	0.88	3	-
GCF_000739995.1	s__Giesbergeria granuli	81.3152	558	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_000204645.1	s__Alicycliphilus denitrificans	81.2852	614	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.9844	575	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	80.4283	592	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_002176815.1	s__Acidovorax sp002176815	80.4065	531	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCA_001770955.1	s__Giesbergeria sp001770955	80.1982	490	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_001633105.1	s__Acidovorax sp001633105	80.0597	557	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	80.0054	412	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620245.1	s__Acidovorax sp011620245	79.9399	334	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	79.9369	489	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCF_002245625.1	s__Acidovorax kalamii	79.8677	555	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001714725.1	s__Acidovorax sp001714725	79.5958	516	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003951285.1	s__Variovorax beijingensis	79.4991	498	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.27	99.27	0.92	0.92	2	-
GCF_000463015.1	s__Variovorax paradoxus_E	79.2521	498	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.39	98.39	0.87	0.87	2	-
GCF_004363315.1	s__Tepidicella xavieri	79.1726	334	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	79.1574	330	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	79.064	400	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,747] [INFO] GTDB search result was written to GCF_003337425.1_ASM333742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:15,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:15,753] [INFO] DFAST_QC result json was written to GCF_003337425.1_ASM333742v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:15,754] [INFO] DFAST_QC completed!
[2024-01-24 12:15:15,754] [INFO] Total running time: 0h1m25s