[2023-06-16 23:13:20,665] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:13:20,667] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:13:20,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference
[2023-06-16 23:13:21,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:13:21,960] [INFO] Task started: Prodigal
[2023-06-16 23:13:21,960] [INFO] Running command: gunzip -c /var/lib/cwl/stg36fa2e12-214f-4a79-bb93-64ee224a9e12/GCA_009926355.1_ASM992635v1_genomic.fna.gz | prodigal -d GCA_009926355.1_ASM992635v1_genomic.fna/cds.fna -a GCA_009926355.1_ASM992635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:13:30,325] [INFO] Task succeeded: Prodigal
[2023-06-16 23:13:30,325] [INFO] Task started: HMMsearch
[2023-06-16 23:13:30,326] [INFO] Running command: hmmsearch --tblout GCA_009926355.1_ASM992635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/reference_markers.hmm GCA_009926355.1_ASM992635v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:13:30,611] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:13:30,612] [INFO] Found 6/6 markers.
[2023-06-16 23:13:30,646] [INFO] Query marker FASTA was written to GCA_009926355.1_ASM992635v1_genomic.fna/markers.fasta
[2023-06-16 23:13:30,646] [INFO] Task started: Blastn
[2023-06-16 23:13:30,647] [INFO] Running command: blastn -query GCA_009926355.1_ASM992635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/reference_markers.fasta -out GCA_009926355.1_ASM992635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:13:31,436] [INFO] Task succeeded: Blastn
[2023-06-16 23:13:31,441] [INFO] Selected 29 target genomes.
[2023-06-16 23:13:31,441] [INFO] Target genome list was writen to GCA_009926355.1_ASM992635v1_genomic.fna/target_genomes.txt
[2023-06-16 23:13:31,458] [INFO] Task started: fastANI
[2023-06-16 23:13:31,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg36fa2e12-214f-4a79-bb93-64ee224a9e12/GCA_009926355.1_ASM992635v1_genomic.fna.gz --refList GCA_009926355.1_ASM992635v1_genomic.fna/target_genomes.txt --output GCA_009926355.1_ASM992635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:13:48,769] [INFO] Task succeeded: fastANI
[2023-06-16 23:13:48,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:13:48,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:13:48,794] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:13:48,795] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 23:13:48,795] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.2262	154	695	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.2226	138	695	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.062	139	695	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.0148	138	695	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	76.9443	126	695	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	76.915	128	695	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8926	165	695	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.8355	169	695	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	76.7788	134	695	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	76.695	100	695	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.6743	83	695	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.6454	138	695	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	76.6403	123	695	95	below_threshold
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	76.6256	99	695	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.6108	97	695	95	below_threshold
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	76.6006	99	695	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	76.5996	101	695	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	76.5771	117	695	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	76.5763	117	695	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	76.5695	107	695	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	76.5678	103	695	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	76.5608	100	695	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	76.4971	79	695	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.4905	100	695	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	76.4771	101	695	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	76.471	80	695	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	76.0844	101	695	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	75.8075	64	695	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 23:13:48,797] [INFO] DFAST Taxonomy check result was written to GCA_009926355.1_ASM992635v1_genomic.fna/tc_result.tsv
[2023-06-16 23:13:48,797] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:13:48,798] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:13:48,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/checkm_data
[2023-06-16 23:13:48,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:13:48,827] [INFO] Task started: CheckM
[2023-06-16 23:13:48,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009926355.1_ASM992635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009926355.1_ASM992635v1_genomic.fna/checkm_input GCA_009926355.1_ASM992635v1_genomic.fna/checkm_result
[2023-06-16 23:14:19,894] [INFO] Task succeeded: CheckM
[2023-06-16 23:14:19,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:14:19,921] [INFO] ===== Completeness check finished =====
[2023-06-16 23:14:19,921] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:14:19,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009926355.1_ASM992635v1_genomic.fna/markers.fasta)
[2023-06-16 23:14:19,922] [INFO] Task started: Blastn
[2023-06-16 23:14:19,922] [INFO] Running command: blastn -query GCA_009926355.1_ASM992635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg584a7124-54f1-4824-bb94-0161d99bc6d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_009926355.1_ASM992635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:14:21,226] [INFO] Task succeeded: Blastn
[2023-06-16 23:14:21,231] [INFO] Selected 29 target genomes.
[2023-06-16 23:14:21,231] [INFO] Target genome list was writen to GCA_009926355.1_ASM992635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:14:21,339] [INFO] Task started: fastANI
[2023-06-16 23:14:21,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg36fa2e12-214f-4a79-bb93-64ee224a9e12/GCA_009926355.1_ASM992635v1_genomic.fna.gz --refList GCA_009926355.1_ASM992635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009926355.1_ASM992635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:14:38,382] [INFO] Task succeeded: fastANI
[2023-06-16 23:14:38,407] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:14:38,407] [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_002342165.1	s__Hylemonella sp002342165	98.9323	426	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.18	99.01	0.79	0.72	4	conclusive
GCA_002454975.1	s__Hylemonella sp002454975	77.9399	202	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	77.3172	160	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCA_018882835.1	s__Limnohabitans sp018882835	77.2601	139	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837235.1	s__Limnohabitans_A sp014837235	77.2416	137	695	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_002778275.1	s__Limnohabitans_A sp002778275	77.2088	161	695	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_003063355.1	s__Limnohabitans_A sp003063355	77.1643	172	695	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_903932865.1	s__Limnohabitans_A sp903932865	77.1425	162	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.93	99.93	0.98	0.98	2	-
GCA_001771065.1	s__Rhodoferax sp001771065	77.0488	111	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592265.1	s__Hylemonella delicata	77.0255	153	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	77.0048	147	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823635.1	s__UBA2334 sp013823635	76.9607	122	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013334205.1	s__Hylemonella sp013334205	76.9566	146	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503365.1	s__Hydrogenophaga sp005503365	76.9457	102	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001432305.1	s__Hylemonella sp001432305	76.9231	147	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416775.1	s__Rhodoferax sp013416775	76.8945	120	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415675.1	s__Rhodoferax sp003415675	76.8926	165	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663825.1	s__Acidovorax sp003663825	76.8786	147	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405905.1	s__Acidovorax sp005405905	76.8713	142	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987055.1	s__Giesbergeria sp017987055	76.8518	61	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.05	99.05	0.76	0.76	2	-
GCF_001270065.2	s__Limnohabitans_A planktonicus	76.8486	168	695	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_018619435.1	s__Rhodoferax sp018619435	76.8365	116	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110225.1	s__Brachymonas denitrificans	76.6743	83	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953985.1	s__Limnohabitans_A sp903953985	76.6577	113	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.68	98.68	0.76	0.76	2	-
GCF_000204195.1	s__Acidovorax radicis	76.6454	138	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.28	97.43	0.95	0.93	5	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	76.6067	95	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCF_003669015.1	s__Acidovorax sp002754495	76.5145	148	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCA_017988075.1	s__Ramlibacter sp017988075	76.4969	95	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	76.1738	87	695	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:14:38,409] [INFO] GTDB search result was written to GCA_009926355.1_ASM992635v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:14:38,410] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:14:38,420] [INFO] DFAST_QC result json was written to GCA_009926355.1_ASM992635v1_genomic.fna/dqc_result.json
[2023-06-16 23:14:38,420] [INFO] DFAST_QC completed!
[2023-06-16 23:14:38,420] [INFO] Total running time: 0h1m18s