[2023-06-13 11:03:48,668] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:03:48,670] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:03:48,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference
[2023-06-13 11:03:50,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:03:50,044] [INFO] Task started: Prodigal
[2023-06-13 11:03:50,044] [INFO] Running command: gunzip -c /var/lib/cwl/stgd714278f-ae21-4730-af28-bf37dbb9c8cd/GCA_022705245.1_ASM2270524v1_genomic.fna.gz | prodigal -d GCA_022705245.1_ASM2270524v1_genomic.fna/cds.fna -a GCA_022705245.1_ASM2270524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:04:04,145] [INFO] Task succeeded: Prodigal
[2023-06-13 11:04:04,146] [INFO] Task started: HMMsearch
[2023-06-13 11:04:04,146] [INFO] Running command: hmmsearch --tblout GCA_022705245.1_ASM2270524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/reference_markers.hmm GCA_022705245.1_ASM2270524v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:04:04,456] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:04:04,458] [INFO] Found 6/6 markers.
[2023-06-13 11:04:04,502] [INFO] Query marker FASTA was written to GCA_022705245.1_ASM2270524v1_genomic.fna/markers.fasta
[2023-06-13 11:04:04,503] [INFO] Task started: Blastn
[2023-06-13 11:04:04,503] [INFO] Running command: blastn -query GCA_022705245.1_ASM2270524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/reference_markers.fasta -out GCA_022705245.1_ASM2270524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:05,569] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:05,574] [INFO] Selected 30 target genomes.
[2023-06-13 11:04:05,575] [INFO] Target genome list was writen to GCA_022705245.1_ASM2270524v1_genomic.fna/target_genomes.txt
[2023-06-13 11:04:05,578] [INFO] Task started: fastANI
[2023-06-13 11:04:05,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgd714278f-ae21-4730-af28-bf37dbb9c8cd/GCA_022705245.1_ASM2270524v1_genomic.fna.gz --refList GCA_022705245.1_ASM2270524v1_genomic.fna/target_genomes.txt --output GCA_022705245.1_ASM2270524v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:04:32,666] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:32,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:04:32,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:04:32,695] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:04:32,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:04:32,696] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.3933	601	1355	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.2055	566	1355	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.1474	521	1355	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	80.1247	610	1355	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.1019	538	1355	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	80.0372	585	1355	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	80.031	583	1355	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.023	557	1355	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	79.9982	594	1355	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.9325	563	1355	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8829	584	1355	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.8717	599	1355	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.7956	595	1355	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	79.7482	502	1355	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.7252	586	1355	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	79.7143	500	1355	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	79.6414	513	1355	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	79.6395	533	1355	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.5878	528	1355	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.4962	430	1355	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	79.4897	483	1355	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	79.4769	432	1355	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.4659	505	1355	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	79.4356	504	1355	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.3782	444	1355	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.256	522	1355	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.2063	444	1355	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	79.0696	469	1355	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	78.7215	438	1355	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	78.6409	437	1355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:04:32,698] [INFO] DFAST Taxonomy check result was written to GCA_022705245.1_ASM2270524v1_genomic.fna/tc_result.tsv
[2023-06-13 11:04:32,699] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:04:32,699] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:04:32,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/checkm_data
[2023-06-13 11:04:32,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:04:32,748] [INFO] Task started: CheckM
[2023-06-13 11:04:32,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022705245.1_ASM2270524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022705245.1_ASM2270524v1_genomic.fna/checkm_input GCA_022705245.1_ASM2270524v1_genomic.fna/checkm_result
[2023-06-13 11:05:24,131] [INFO] Task succeeded: CheckM
[2023-06-13 11:05:24,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-13 11:05:24,162] [INFO] ===== Completeness check finished =====
[2023-06-13 11:05:24,162] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:05:24,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022705245.1_ASM2270524v1_genomic.fna/markers.fasta)
[2023-06-13 11:05:24,163] [INFO] Task started: Blastn
[2023-06-13 11:05:24,163] [INFO] Running command: blastn -query GCA_022705245.1_ASM2270524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0859f487-9b22-4ffe-8b99-bb06775fb929/dqc_reference/reference_markers_gtdb.fasta -out GCA_022705245.1_ASM2270524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:05:26,118] [INFO] Task succeeded: Blastn
[2023-06-13 11:05:26,124] [INFO] Selected 23 target genomes.
[2023-06-13 11:05:26,124] [INFO] Target genome list was writen to GCA_022705245.1_ASM2270524v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:05:26,135] [INFO] Task started: fastANI
[2023-06-13 11:05:26,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgd714278f-ae21-4730-af28-bf37dbb9c8cd/GCA_022705245.1_ASM2270524v1_genomic.fna.gz --refList GCA_022705245.1_ASM2270524v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022705245.1_ASM2270524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:05:45,573] [INFO] Task succeeded: fastANI
[2023-06-13 11:05:45,594] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:05:45,594] [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_016721925.1	s__JAABQG01 sp016721925	98.0351	1223	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	conclusive
GCA_011391595.1	s__JAABQG01 sp011391595	84.0921	794	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391155.1	s__JAABQG01 sp011391155	83.275	644	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879655.1	s__JAABQG01 sp014879655	81.0469	629	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.6783	526	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	80.6417	550	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	80.5697	561	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	80.1957	567	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_001432305.1	s__Hylemonella sp001432305	80.1706	538	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	80.1677	562	1355	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_001592305.1	s__Hydrogenophaga taeniospiralis	80.1584	606	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013334205.1	s__Hylemonella sp013334205	80.1272	563	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842205.1	s__PHCI01 sp002842205	80.1101	598	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	80.1075	501	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006970865.1	s__Rhodoferax_A sediminis	80.0766	550	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381265.1	s__Curvibacter lanceolatus	80.0603	580	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
GCA_016185015.1	s__Hylemonella sp016185015	80.0445	522	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013423955.1	s__Ottowia beijingensis	79.9853	596	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	97.71	97.71	0.88	0.88	2	-
GCF_014652235.1	s__Pseudorhodoferax aquiterrae	79.8536	601	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	79.8065	508	1355	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_001421705.1	s__Xylophilus sp001421705	79.537	511	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663825.1	s__Acidovorax sp003663825	79.2098	481	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828125.1	s__Acidovorax sp018828125	79.1274	485	1355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.50	98.69	0.98	0.93	11	-
--------------------------------------------------------------------------------
[2023-06-13 11:05:45,597] [INFO] GTDB search result was written to GCA_022705245.1_ASM2270524v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:05:45,597] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:05:45,603] [INFO] DFAST_QC result json was written to GCA_022705245.1_ASM2270524v1_genomic.fna/dqc_result.json
[2023-06-13 11:05:45,603] [INFO] DFAST_QC completed!
[2023-06-13 11:05:45,603] [INFO] Total running time: 0h1m57s