[2024-01-24 12:23:03,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,538] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference
[2024-01-24 12:23:04,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,801] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a91df27-918f-4953-8fcf-fef6b7697288/GCF_028023875.1_ASM2802387v1_genomic.fna.gz | prodigal -d GCF_028023875.1_ASM2802387v1_genomic.fna/cds.fna -a GCF_028023875.1_ASM2802387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:21,594] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:21,595] [INFO] Task started: HMMsearch
[2024-01-24 12:23:21,595] [INFO] Running command: hmmsearch --tblout GCF_028023875.1_ASM2802387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/reference_markers.hmm GCF_028023875.1_ASM2802387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:21,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:21,894] [INFO] Found 6/6 markers.
[2024-01-24 12:23:21,940] [INFO] Query marker FASTA was written to GCF_028023875.1_ASM2802387v1_genomic.fna/markers.fasta
[2024-01-24 12:23:21,940] [INFO] Task started: Blastn
[2024-01-24 12:23:21,941] [INFO] Running command: blastn -query GCF_028023875.1_ASM2802387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/reference_markers.fasta -out GCF_028023875.1_ASM2802387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:22,996] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:23,000] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:23,000] [INFO] Target genome list was writen to GCF_028023875.1_ASM2802387v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:23,006] [INFO] Task started: fastANI
[2024-01-24 12:23:23,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a91df27-918f-4953-8fcf-fef6b7697288/GCF_028023875.1_ASM2802387v1_genomic.fna.gz --refList GCF_028023875.1_ASM2802387v1_genomic.fna/target_genomes.txt --output GCF_028023875.1_ASM2802387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:42,713] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:42,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:42,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:42,732] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:42,732] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:42,732] [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
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.0329	911	1661	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	82.6562	981	1661	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	82.6365	1018	1661	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	82.496	1045	1661	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	82.4641	1008	1661	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	82.2153	851	1661	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	82.1569	1026	1661	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.952	692	1661	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9228	760	1661	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.9208	738	1661	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.8868	688	1661	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.7995	753	1661	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.6263	766	1661	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.5165	644	1661	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.4101	729	1661	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.7671	662	1661	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	78.8039	429	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:42,734] [INFO] DFAST Taxonomy check result was written to GCF_028023875.1_ASM2802387v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:42,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:42,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:42,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/checkm_data
[2024-01-24 12:23:42,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:42,782] [INFO] Task started: CheckM
[2024-01-24 12:23:42,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028023875.1_ASM2802387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028023875.1_ASM2802387v1_genomic.fna/checkm_input GCF_028023875.1_ASM2802387v1_genomic.fna/checkm_result
[2024-01-24 12:25:32,471] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:32,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:32,491] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:32,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:32,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028023875.1_ASM2802387v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:32,492] [INFO] Task started: Blastn
[2024-01-24 12:25:32,492] [INFO] Running command: blastn -query GCF_028023875.1_ASM2802387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfe2325f-5a16-4944-9100-e362c81486d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_028023875.1_ASM2802387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:34,607] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:34,612] [INFO] Selected 18 target genomes.
[2024-01-24 12:25:34,612] [INFO] Target genome list was writen to GCF_028023875.1_ASM2802387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:34,635] [INFO] Task started: fastANI
[2024-01-24 12:25:34,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a91df27-918f-4953-8fcf-fef6b7697288/GCF_028023875.1_ASM2802387v1_genomic.fna.gz --refList GCF_028023875.1_ASM2802387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028023875.1_ASM2802387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:59,485] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:59,504] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:59,504] [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_000745855.1	s__Xenophilus azovorans	84.6422	1072	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241185.1	s__ALPHA2B sp018241185	84.156	993	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	84.1393	1096	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	84.1363	1112	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875635.1	s__ALPHA2B sp901875635	84.0681	1050	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	99.68	99.68	0.89	0.89	2	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	83.8706	986	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864295.1	s__Pseudacidovorax sp903864295	83.4707	1078	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	97.16	95.11	0.92	0.86	4	-
GCF_014170375.1	s__Variovorax sp014170375	83.1257	1057	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217005.1	s__Variovorax sp004217005	82.8095	964	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.70	99.70	0.95	0.95	2	-
GCF_001591365.1	s__Variovorax paradoxus	82.6537	982	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.93	98.38	0.94	0.90	4	-
GCF_900112425.1	s__Variovorax sp900112425	82.5411	1108	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.32	98.64	0.96	0.91	3	-
GCF_013376045.1	s__Variovorax sp013376045	82.5139	1010	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016082275.1	s__Variovorax sp016082275	82.4383	1029	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216615.1	s__Variovorax sp004216615	82.2389	1005	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	81.7099	737	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_007677875.1	s__Pseudorhodoferax boronicumulans_A	81.589	947	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765735.1	s__Variovorax sp009765735	81.5243	868	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241325.1	s__Ottowia sp018241325	80.1291	650	1661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:59,506] [INFO] GTDB search result was written to GCF_028023875.1_ASM2802387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:59,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:59,514] [INFO] DFAST_QC result json was written to GCF_028023875.1_ASM2802387v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:59,514] [INFO] DFAST_QC completed!
[2024-01-24 12:25:59,515] [INFO] Total running time: 0h2m56s