[2023-06-29 04:41:39,194] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:39,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:39,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference
[2023-06-29 04:41:42,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:42,376] [INFO] Task started: Prodigal
[2023-06-29 04:41:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg189474c9-ed23-4ff2-8b93-0ccecc6cadba/GCA_020048405.1_ASM2004840v1_genomic.fna.gz | prodigal -d GCA_020048405.1_ASM2004840v1_genomic.fna/cds.fna -a GCA_020048405.1_ASM2004840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:55,585] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:55,586] [INFO] Task started: HMMsearch
[2023-06-29 04:41:55,586] [INFO] Running command: hmmsearch --tblout GCA_020048405.1_ASM2004840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/reference_markers.hmm GCA_020048405.1_ASM2004840v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:55,996] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:55,997] [INFO] Found 6/6 markers.
[2023-06-29 04:41:56,031] [INFO] Query marker FASTA was written to GCA_020048405.1_ASM2004840v1_genomic.fna/markers.fasta
[2023-06-29 04:41:56,031] [INFO] Task started: Blastn
[2023-06-29 04:41:56,032] [INFO] Running command: blastn -query GCA_020048405.1_ASM2004840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/reference_markers.fasta -out GCA_020048405.1_ASM2004840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:56,861] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:56,865] [INFO] Selected 32 target genomes.
[2023-06-29 04:41:56,866] [INFO] Target genome list was writen to GCA_020048405.1_ASM2004840v1_genomic.fna/target_genomes.txt
[2023-06-29 04:41:56,886] [INFO] Task started: fastANI
[2023-06-29 04:41:56,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg189474c9-ed23-4ff2-8b93-0ccecc6cadba/GCA_020048405.1_ASM2004840v1_genomic.fna.gz --refList GCA_020048405.1_ASM2004840v1_genomic.fna/target_genomes.txt --output GCA_020048405.1_ASM2004840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:21,677] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:21,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:21,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:21,705] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:21,706] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:21,706] [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 taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	79.151	438	1080	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.0834	336	1080	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	79.0301	456	1080	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	78.9392	396	1080	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	78.9347	331	1080	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	78.8894	401	1080	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	78.8675	337	1080	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.7865	317	1080	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	78.7862	358	1080	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.7706	391	1080	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.7006	376	1080	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	78.6608	376	1080	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6205	330	1080	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	78.6126	381	1080	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	78.6015	379	1080	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	78.5853	301	1080	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	78.5277	296	1080	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	78.5134	382	1080	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.4844	354	1080	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	78.4816	304	1080	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	78.4646	343	1080	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	78.2156	295	1080	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	78.0828	287	1080	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	77.9322	323	1080	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.9247	298	1080	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	77.9247	321	1080	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.8563	290	1080	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	77.8009	247	1080	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.6567	231	1080	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.6007	226	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:21,708] [INFO] DFAST Taxonomy check result was written to GCA_020048405.1_ASM2004840v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:21,709] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:21,709] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:21,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/checkm_data
[2023-06-29 04:42:21,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:21,751] [INFO] Task started: CheckM
[2023-06-29 04:42:21,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020048405.1_ASM2004840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020048405.1_ASM2004840v1_genomic.fna/checkm_input GCA_020048405.1_ASM2004840v1_genomic.fna/checkm_result
[2023-06-29 04:43:16,034] [INFO] Task succeeded: CheckM
[2023-06-29 04:43:16,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:43:16,058] [INFO] ===== Completeness check finished =====
[2023-06-29 04:43:16,058] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:43:16,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020048405.1_ASM2004840v1_genomic.fna/markers.fasta)
[2023-06-29 04:43:16,059] [INFO] Task started: Blastn
[2023-06-29 04:43:16,059] [INFO] Running command: blastn -query GCA_020048405.1_ASM2004840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ef2218-8acc-4e70-98fd-f45595a7e229/dqc_reference/reference_markers_gtdb.fasta -out GCA_020048405.1_ASM2004840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:43:17,426] [INFO] Task succeeded: Blastn
[2023-06-29 04:43:17,431] [INFO] Selected 30 target genomes.
[2023-06-29 04:43:17,431] [INFO] Target genome list was writen to GCA_020048405.1_ASM2004840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:43:17,450] [INFO] Task started: fastANI
[2023-06-29 04:43:17,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg189474c9-ed23-4ff2-8b93-0ccecc6cadba/GCA_020048405.1_ASM2004840v1_genomic.fna.gz --refList GCA_020048405.1_ASM2004840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020048405.1_ASM2004840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:43:39,282] [INFO] Task succeeded: fastANI
[2023-06-29 04:43:39,308] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:43:39,308] [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_903928495.1	s__UBA2334 sp903928495	91.0748	814	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	99.91	99.91	0.98	0.98	2	-
GCA_013823635.1	s__UBA2334 sp013823635	81.3659	512	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344885.1	s__UBA2334 sp002344885	80.5973	509	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837145.1	s__BK-30 sp002837145	79.5122	374	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	79.1539	451	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333605.1	s__Hydrogenophaga sp018333605	79.0482	255	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	79.0395	455	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	79.0216	389	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	79.0005	419	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001205.1	s__Hydrogenophaga sp002001205	78.958	429	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268905.1	s__Acidovorax defluvii	78.9287	356	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.35	96.64	0.82	0.75	12	-
GCF_002245625.1	s__Acidovorax kalamii	78.9283	397	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	78.8946	422	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	78.8937	330	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823505.1	s__Hydrogenophaga sp013823505	78.8771	393	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842205.1	s__PHCI01 sp002842205	78.6931	349	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	78.6331	387	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	78.6169	361	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	78.5764	334	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
GCF_014489595.1	s__Acidovorax_F monticola	78.5663	349	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCA_018335615.1	s__Hydrogenophaga sp018335615	78.5657	293	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	78.5476	323	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCF_003053545.1	s__Acidovorax sp003053545	78.3622	399	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_018241405.1	s__Alicycliphilus sp018241405	78.2957	294	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCF_016428875.1	s__Xylophilus sp016428875	78.19	281	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241325.1	s__Ottowia sp018241325	78.0739	271	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017535.1	s__Ottowia sp008017535	78.0072	272	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054745.1	s__Alicycliphilus sp018054745	77.9752	254	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.31	99.29	0.86	0.83	3	-
GCF_001598795.1	s__Comamonas acidovorans	77.9144	322	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	-
GCF_004364775.1	s__Comamonas sp004364775	77.6204	249	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:43:39,311] [INFO] GTDB search result was written to GCA_020048405.1_ASM2004840v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:43:39,311] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:43:39,317] [INFO] DFAST_QC result json was written to GCA_020048405.1_ASM2004840v1_genomic.fna/dqc_result.json
[2023-06-29 04:43:39,317] [INFO] DFAST_QC completed!
[2023-06-29 04:43:39,317] [INFO] Total running time: 0h2m0s