[2024-01-24 12:47:22,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference
[2024-01-24 12:47:24,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:24,135] [INFO] Task started: Prodigal
[2024-01-24 12:47:24,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg72f94f59-fb88-4a39-8ec1-84231a0c7286/GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna.gz | prodigal -d GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/cds.fna -a GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:31,295] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:31,296] [INFO] Task started: HMMsearch
[2024-01-24 12:47:31,296] [INFO] Running command: hmmsearch --tblout GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/reference_markers.hmm GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:31,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:31,581] [INFO] Found 6/6 markers.
[2024-01-24 12:47:31,605] [INFO] Query marker FASTA was written to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/markers.fasta
[2024-01-24 12:47:31,605] [INFO] Task started: Blastn
[2024-01-24 12:47:31,605] [INFO] Running command: blastn -query GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/reference_markers.fasta -out GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:32,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:32,369] [INFO] Selected 30 target genomes.
[2024-01-24 12:47:32,369] [INFO] Target genome list was writen to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/target_genomes.txt
[2024-01-24 12:47:32,394] [INFO] Task started: fastANI
[2024-01-24 12:47:32,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg72f94f59-fb88-4a39-8ec1-84231a0c7286/GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna.gz --refList GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/target_genomes.txt --output GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:57,244] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:57,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:57,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:57,262] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:57,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:57,262] [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
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	77.6343	50	829	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	77.0579	51	829	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	76.959	56	829	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	76.9135	52	829	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	76.9083	52	829	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	76.8569	53	829	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	76.8329	55	829	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.7525	53	829	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	76.4488	64	829	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	76.4021	50	829	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	76.3033	63	829	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.2877	62	829	95	below_threshold
Janthinobacterium agaricidamnosum	strain=NBRC 102515	GCA_001571185.1	55508	55508	type	True	76.1366	58	829	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:57,264] [INFO] DFAST Taxonomy check result was written to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/tc_result.tsv
[2024-01-24 12:47:57,264] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:57,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:57,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/checkm_data
[2024-01-24 12:47:57,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:57,293] [INFO] Task started: CheckM
[2024-01-24 12:47:57,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/checkm_input GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/checkm_result
[2024-01-24 12:48:24,573] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:24,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:24,595] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:24,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:24,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/markers.fasta)
[2024-01-24 12:48:24,597] [INFO] Task started: Blastn
[2024-01-24 12:48:24,597] [INFO] Running command: blastn -query GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf47a232f-90f3-4c6f-a586-74a618244cc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:25,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:25,839] [INFO] Selected 16 target genomes.
[2024-01-24 12:48:25,840] [INFO] Target genome list was writen to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:25,886] [INFO] Task started: fastANI
[2024-01-24 12:48:25,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg72f94f59-fb88-4a39-8ec1-84231a0c7286/GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna.gz --refList GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:36,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:36,231] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:36,231] [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_000158475.2	s__Oxalobacter formigenes_B	100.0	828	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCA_900760095.1	s__Oxalobacter sp900760095	80.3698	432	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127965.1	s__Oxalobacter formigenes	79.191	344	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	99.83	99.22	0.99	0.98	6	-
GCA_905202055.1	s__Oxalobacter sp905202055	78.7701	326	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213425.1	s__Herbaspirillum aquaticum	76.8569	53	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	-
GCF_000577615.1	s__Herbaspirillum sp000577615	76.6522	62	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524145.1	s__Oxalobacter sp017524145	76.0963	66	829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:36,233] [INFO] GTDB search result was written to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:36,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:36,237] [INFO] DFAST_QC result json was written to GCF_000158475.2_Oxal_for_HOxBLS_2_V2_genomic.fna/dqc_result.json
[2024-01-24 12:48:36,237] [INFO] DFAST_QC completed!
[2024-01-24 12:48:36,237] [INFO] Total running time: 0h1m13s