[2024-01-24 12:29:21,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:21,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:21,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference
[2024-01-24 12:29:22,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:22,962] [INFO] Task started: Prodigal
[2024-01-24 12:29:22,962] [INFO] Running command: gunzip -c /var/lib/cwl/stga94c3663-9038-4f55-9a33-575f51c92b11/GCF_016894385.1_ASM1689438v1_genomic.fna.gz | prodigal -d GCF_016894385.1_ASM1689438v1_genomic.fna/cds.fna -a GCF_016894385.1_ASM1689438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:45,065] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:45,065] [INFO] Task started: HMMsearch
[2024-01-24 12:29:45,065] [INFO] Running command: hmmsearch --tblout GCF_016894385.1_ASM1689438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/reference_markers.hmm GCF_016894385.1_ASM1689438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:45,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:45,404] [INFO] Found 6/6 markers.
[2024-01-24 12:29:45,461] [INFO] Query marker FASTA was written to GCF_016894385.1_ASM1689438v1_genomic.fna/markers.fasta
[2024-01-24 12:29:45,461] [INFO] Task started: Blastn
[2024-01-24 12:29:45,461] [INFO] Running command: blastn -query GCF_016894385.1_ASM1689438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/reference_markers.fasta -out GCF_016894385.1_ASM1689438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:46,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:46,562] [INFO] Selected 12 target genomes.
[2024-01-24 12:29:46,562] [INFO] Target genome list was writen to GCF_016894385.1_ASM1689438v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:46,571] [INFO] Task started: fastANI
[2024-01-24 12:29:46,572] [INFO] Running command: fastANI --query /var/lib/cwl/stga94c3663-9038-4f55-9a33-575f51c92b11/GCF_016894385.1_ASM1689438v1_genomic.fna.gz --refList GCF_016894385.1_ASM1689438v1_genomic.fna/target_genomes.txt --output GCF_016894385.1_ASM1689438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:08,370] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:08,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:08,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:08,389] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:08,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:08,390] [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 oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	100.0	2231	2231	95	conclusive
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	99.9716	2184	2231	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	88.8841	1482	2231	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	88.8583	1506	2231	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	88.7775	1535	2231	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	88.7125	1512	2231	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	88.219	1546	2231	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	84.7798	1466	2231	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.6431	795	2231	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.6185	562	2231	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.5529	686	2231	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	77.9542	597	2231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:08,391] [INFO] DFAST Taxonomy check result was written to GCF_016894385.1_ASM1689438v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:08,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:08,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:08,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/checkm_data
[2024-01-24 12:30:08,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:08,459] [INFO] Task started: CheckM
[2024-01-24 12:30:08,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016894385.1_ASM1689438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016894385.1_ASM1689438v1_genomic.fna/checkm_input GCF_016894385.1_ASM1689438v1_genomic.fna/checkm_result
[2024-01-24 12:31:25,398] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:25,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:25,426] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:25,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:25,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016894385.1_ASM1689438v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:25,427] [INFO] Task started: Blastn
[2024-01-24 12:31:25,427] [INFO] Running command: blastn -query GCF_016894385.1_ASM1689438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08c94c3e-6055-4006-bd50-342201ea668b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016894385.1_ASM1689438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:27,591] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:27,596] [INFO] Selected 7 target genomes.
[2024-01-24 12:31:27,596] [INFO] Target genome list was writen to GCF_016894385.1_ASM1689438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:27,603] [INFO] Task started: fastANI
[2024-01-24 12:31:27,603] [INFO] Running command: fastANI --query /var/lib/cwl/stga94c3663-9038-4f55-9a33-575f51c92b11/GCF_016894385.1_ASM1689438v1_genomic.fna.gz --refList GCF_016894385.1_ASM1689438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016894385.1_ASM1689438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:42,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:42,840] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:42,840] [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_016894385.1	s__Cupriavidus oxalaticus	100.0	2231	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.73	98.93	0.98	0.92	5	conclusive
GCF_004768545.1	s__Cupriavidus oxalaticus_A	94.0585	1773	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.89	98.53	0.88	0.85	3	-
GCF_000426345.1	s__Cupriavidus sp000426345	93.9516	1688	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
GCF_017814975.1	s__Cupriavidus sp017814975	93.4616	1703	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402535.1	s__Cupriavidus sp003402535	92.835	1794	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	88.9045	1582	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_000744095.1	s__Cupriavidus necator_A	88.8488	1641	2231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,842] [INFO] GTDB search result was written to GCF_016894385.1_ASM1689438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:42,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:42,846] [INFO] DFAST_QC result json was written to GCF_016894385.1_ASM1689438v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:42,846] [INFO] DFAST_QC completed!
[2024-01-24 12:31:42,846] [INFO] Total running time: 0h2m21s