[2024-01-24 13:46:01,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,277] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference
[2024-01-24 13:46:02,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,626] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg00f3259d-786f-4051-bf29-d05882e783a3/GCF_000372525.1_ASM37252v1_genomic.fna.gz | prodigal -d GCF_000372525.1_ASM37252v1_genomic.fna/cds.fna -a GCF_000372525.1_ASM37252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:23,779] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:23,779] [INFO] Task started: HMMsearch
[2024-01-24 13:46:23,779] [INFO] Running command: hmmsearch --tblout GCF_000372525.1_ASM37252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/reference_markers.hmm GCF_000372525.1_ASM37252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:24,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:24,137] [INFO] Found 6/6 markers.
[2024-01-24 13:46:24,192] [INFO] Query marker FASTA was written to GCF_000372525.1_ASM37252v1_genomic.fna/markers.fasta
[2024-01-24 13:46:24,193] [INFO] Task started: Blastn
[2024-01-24 13:46:24,193] [INFO] Running command: blastn -query GCF_000372525.1_ASM37252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/reference_markers.fasta -out GCF_000372525.1_ASM37252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:25,304] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:25,304] [INFO] Target genome list was writen to GCF_000372525.1_ASM37252v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,345] [INFO] Task started: fastANI
[2024-01-24 13:46:25,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg00f3259d-786f-4051-bf29-d05882e783a3/GCF_000372525.1_ASM37252v1_genomic.fna.gz --refList GCF_000372525.1_ASM37252v1_genomic.fna/target_genomes.txt --output GCF_000372525.1_ASM37252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:45,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:45,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:45,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:45,182] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:45,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:45,183] [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
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	100.0	2201	2208	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	94.4153	1683	2208	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	94.3326	1750	2208	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	94.3008	1837	2208	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	89.5745	1608	2208	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	88.6326	1523	2208	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	84.8188	1388	2208	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.6023	819	2208	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	78.5218	589	2208	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.3839	687	2208	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.105	581	2208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,185] [INFO] DFAST Taxonomy check result was written to GCF_000372525.1_ASM37252v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:45,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:45,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:45,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/checkm_data
[2024-01-24 13:46:45,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:45,252] [INFO] Task started: CheckM
[2024-01-24 13:46:45,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372525.1_ASM37252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372525.1_ASM37252v1_genomic.fna/checkm_input GCF_000372525.1_ASM37252v1_genomic.fna/checkm_result
[2024-01-24 13:47:53,746] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:53,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:53,771] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:53,771] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:53,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372525.1_ASM37252v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:53,772] [INFO] Task started: Blastn
[2024-01-24 13:47:53,773] [INFO] Running command: blastn -query GCF_000372525.1_ASM37252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70127bc4-f060-4551-90ee-8c63775cf10f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372525.1_ASM37252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:56,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:56,021] [INFO] Selected 7 target genomes.
[2024-01-24 13:47:56,022] [INFO] Target genome list was writen to GCF_000372525.1_ASM37252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:56,053] [INFO] Task started: fastANI
[2024-01-24 13:47:56,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg00f3259d-786f-4051-bf29-d05882e783a3/GCF_000372525.1_ASM37252v1_genomic.fna.gz --refList GCF_000372525.1_ASM37252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372525.1_ASM37252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:08,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:08,784] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:08,784] [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_000372525.1	s__Cupriavidus neocaledonicus	100.0	2203	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	conclusive
GCF_900250075.1	s__Cupriavidus taiwanensis_C	94.4529	1835	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_001598055.1	s__Cupriavidus nantongensis	94.4103	1684	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	94.3326	1750	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCA_013361545.1	s__Cupriavidus sp013361545	94.326	1166	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.00	99.00	0.84	0.84	2	-
GCF_000069785.1	s__Cupriavidus taiwanensis	94.2901	1837	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCF_900250115.1	s__Cupriavidus taiwanensis_B	94.2836	1879	2208	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.46	95.70	0.97	0.87	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:08,786] [INFO] GTDB search result was written to GCF_000372525.1_ASM37252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:08,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:08,789] [INFO] DFAST_QC result json was written to GCF_000372525.1_ASM37252v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:08,789] [INFO] DFAST_QC completed!
[2024-01-24 13:48:08,789] [INFO] Total running time: 0h2m8s