[2024-01-24 12:06:18,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:18,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:18,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference
[2024-01-24 12:06:19,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:19,248] [INFO] Task started: Prodigal
[2024-01-24 12:06:19,249] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2b68200-e0ed-486e-a180-66ea75600cd5/GCF_006716905.1_ASM671690v1_genomic.fna.gz | prodigal -d GCF_006716905.1_ASM671690v1_genomic.fna/cds.fna -a GCF_006716905.1_ASM671690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:36,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:36,388] [INFO] Task started: HMMsearch
[2024-01-24 12:06:36,388] [INFO] Running command: hmmsearch --tblout GCF_006716905.1_ASM671690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/reference_markers.hmm GCF_006716905.1_ASM671690v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:36,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:36,728] [INFO] Found 6/6 markers.
[2024-01-24 12:06:36,769] [INFO] Query marker FASTA was written to GCF_006716905.1_ASM671690v1_genomic.fna/markers.fasta
[2024-01-24 12:06:36,769] [INFO] Task started: Blastn
[2024-01-24 12:06:36,769] [INFO] Running command: blastn -query GCF_006716905.1_ASM671690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/reference_markers.fasta -out GCF_006716905.1_ASM671690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:37,663] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:37,667] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:37,668] [INFO] Target genome list was writen to GCF_006716905.1_ASM671690v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:37,676] [INFO] Task started: fastANI
[2024-01-24 12:06:37,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b68200-e0ed-486e-a180-66ea75600cd5/GCF_006716905.1_ASM671690v1_genomic.fna.gz --refList GCF_006716905.1_ASM671690v1_genomic.fna/target_genomes.txt --output GCF_006716905.1_ASM671690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,477] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,496] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:53,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:53,496] [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
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	100.0	1544	1547	95	conclusive
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	84.3111	938	1547	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	84.2679	958	1547	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	83.8409	963	1547	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	83.5791	831	1547	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	83.4076	864	1547	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	83.3901	944	1547	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.7322	727	1547	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.6697	718	1547	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.4535	720	1547	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.6344	537	1547	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.4433	537	1547	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.9453	516	1547	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.8776	540	1547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,498] [INFO] DFAST Taxonomy check result was written to GCF_006716905.1_ASM671690v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/checkm_data
[2024-01-24 12:06:53,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:53,549] [INFO] Task started: CheckM
[2024-01-24 12:06:53,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716905.1_ASM671690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716905.1_ASM671690v1_genomic.fna/checkm_input GCF_006716905.1_ASM671690v1_genomic.fna/checkm_result
[2024-01-24 12:07:53,164] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:53,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:53,192] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:53,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:53,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716905.1_ASM671690v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:53,194] [INFO] Task started: Blastn
[2024-01-24 12:07:53,194] [INFO] Running command: blastn -query GCF_006716905.1_ASM671690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606ffd38-3cb0-442d-b375-eb3383ccadd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716905.1_ASM671690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:54,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:54,822] [INFO] Selected 16 target genomes.
[2024-01-24 12:07:54,823] [INFO] Target genome list was writen to GCF_006716905.1_ASM671690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:54,836] [INFO] Task started: fastANI
[2024-01-24 12:07:54,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b68200-e0ed-486e-a180-66ea75600cd5/GCF_006716905.1_ASM671690v1_genomic.fna.gz --refList GCF_006716905.1_ASM671690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716905.1_ASM671690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:13,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:13,738] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:13,739] [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_006716905.1	s__Acidovorax temperans	100.0	1542	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.32	95.61	0.84	0.79	8	conclusive
GCF_003669015.1	s__Acidovorax sp002754495	86.5173	1047	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCA_002377855.1	s__Acidovorax delafieldii_A	86.4322	965	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663825.1	s__Acidovorax sp003663825	86.1258	1040	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633105.1	s__Acidovorax sp001633105	84.897	1009	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302535.1	s__Acidovorax sp000302535	84.755	972	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	-
GCF_003058055.1	s__Acidovorax sp003058055	84.4391	974	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_007993815.1	s__Acidovorax delafieldii	84.2799	955	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_002245625.1	s__Acidovorax kalamii	84.2788	941	1547	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	84.2286	971	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376875.1	s__Acidovorax sp001411535	83.7522	973	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	-
GCF_003060895.1	s__Acidovorax sp003060895	83.7168	834	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204195.1	s__Acidovorax radicis	83.3873	945	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.28	97.43	0.95	0.93	5	-
GCF_000175235.1	s__Acidovorax delafieldii_B	83.1246	703	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464865.1	s__Acidovorax sp001464865	82.7709	756	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	82.6035	944	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:13,741] [INFO] GTDB search result was written to GCF_006716905.1_ASM671690v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:13,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:13,747] [INFO] DFAST_QC result json was written to GCF_006716905.1_ASM671690v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:13,747] [INFO] DFAST_QC completed!
[2024-01-24 12:08:13,747] [INFO] Total running time: 0h1m56s