[2024-01-24 14:14:45,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference
[2024-01-24 14:14:46,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,919] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e6fe7d9-da81-45a2-a4b7-8ec4551d8e0f/GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/cds.fna -a GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:03,118] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:03,119] [INFO] Task started: HMMsearch
[2024-01-24 14:15:03,119] [INFO] Running command: hmmsearch --tblout GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/reference_markers.hmm GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:03,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:03,413] [INFO] Found 6/6 markers.
[2024-01-24 14:15:03,444] [INFO] Query marker FASTA was written to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:15:03,444] [INFO] Task started: Blastn
[2024-01-24 14:15:03,444] [INFO] Running command: blastn -query GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/reference_markers.fasta -out GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:04,272] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:04,280] [INFO] Selected 23 target genomes.
[2024-01-24 14:15:04,281] [INFO] Target genome list was writen to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:15:04,307] [INFO] Task started: fastANI
[2024-01-24 14:15:04,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e6fe7d9-da81-45a2-a4b7-8ec4551d8e0f/GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna.gz --refList GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:23,373] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:23,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:23,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:23,391] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:23,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:23,391] [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
Lampropedia hyalina	strain=DSM 16112	GCA_900129055.1	198706	198706	type	True	100.0	1026	1033	95	conclusive
Corticibacter populi	strain=DSM 105136	GCA_004217315.1	1550736	1550736	type	True	79.1211	437	1033	95	below_threshold
Corticibacter populi	strain=DSM 105136	GCA_003703815.1	1550736	1550736	type	True	79.0771	438	1033	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.5604	341	1033	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	78.5356	303	1033	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.2901	280	1033	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	78.2222	294	1033	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	78.2068	293	1033	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	78.1813	317	1033	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.9478	258	1033	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	77.8594	269	1033	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.8578	311	1033	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	77.7216	290	1033	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	77.633	257	1033	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.5595	287	1033	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.5482	266	1033	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.5405	260	1033	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	77.5256	192	1033	95	below_threshold
Lampropedia aestuarii	strain=YIM MLB12	GCA_004803635.1	2562762	2562762	type	True	77.4143	204	1033	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	77.3462	239	1033	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	77.297	258	1033	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.2681	265	1033	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	77.216	192	1033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:23,393] [INFO] DFAST Taxonomy check result was written to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:23,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:23,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:23,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/checkm_data
[2024-01-24 14:15:23,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:23,430] [INFO] Task started: CheckM
[2024-01-24 14:15:23,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/checkm_input GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:16:12,380] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:12,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:12,416] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:12,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:12,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:16:12,418] [INFO] Task started: Blastn
[2024-01-24 14:16:12,418] [INFO] Running command: blastn -query GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg603a2404-3f18-405d-86e0-4886ff35dfcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:14,089] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:14,093] [INFO] Selected 22 target genomes.
[2024-01-24 14:16:14,093] [INFO] Target genome list was writen to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:14,145] [INFO] Task started: fastANI
[2024-01-24 14:16:14,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e6fe7d9-da81-45a2-a4b7-8ec4551d8e0f/GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna.gz --refList GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:31,859] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:31,882] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:31,883] [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_900129055.1	s__Lampropedia hyalina	100.0	1026	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002285265.1	s__Lampropedia sp002285265	79.1074	381	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	96.24	95.49	0.89	0.89	3	-
GCF_004217315.1	s__Lampropedia populi	79.1016	438	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002285285.1	s__Lampropedia sp002285285	78.9423	372	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	97.35	97.22	0.92	0.90	6	-
GCA_003703475.1	s__Lampropedia sp003703475	78.823	306	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	98.05	97.54	0.92	0.91	4	-
GCF_000739995.1	s__Giesbergeria granuli	78.4013	296	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_012932145.1	s__Giesbergeria sp012932145	78.3468	264	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_019233055.1	s__Curvibacter sp019233055	78.2995	237	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	78.2883	329	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107605.1	s__Acidovorax soli	78.2671	281	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCF_001424425.1	s__Acidovorax sp001424425	78.0295	307	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_003013695.1	s__Pulveribacter suum	78.0156	290	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424265.1	s__Acidovorax_A sp001424265	78.0053	303	1033	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_003663825.1	s__Acidovorax sp003663825	77.7465	282	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002894305.1	s__Comamonas_C sp002894305	77.664	274	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364775.1	s__Comamonas sp004364775	77.6124	283	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076495.1	s__Comamonas koreensis	77.5939	275	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.44	95.11	0.92	0.89	4	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	77.5189	191	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803635.1	s__Lampropedia aestuarii	77.4143	204	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144865.1	s__Ramlibacter sp004144865	77.3262	216	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	77.2749	260	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	77.2691	265	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:31,887] [INFO] GTDB search result was written to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:31,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:31,892] [INFO] DFAST_QC result json was written to GCF_900129055.1_IMG-taxon_2582581266_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:16:31,893] [INFO] DFAST_QC completed!
[2024-01-24 14:16:31,893] [INFO] Total running time: 0h1m46s