[2024-01-24 13:40:28,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference
[2024-01-24 13:40:31,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,148] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e7484a9-69db-4e16-bba3-926cfc893662/GCF_003353055.1_ASM335305v1_genomic.fna.gz | prodigal -d GCF_003353055.1_ASM335305v1_genomic.fna/cds.fna -a GCF_003353055.1_ASM335305v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,028] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,029] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,029] [INFO] Running command: hmmsearch --tblout GCF_003353055.1_ASM335305v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/reference_markers.hmm GCF_003353055.1_ASM335305v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,449] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,525] [INFO] Query marker FASTA was written to GCF_003353055.1_ASM335305v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,526] [INFO] Task started: Blastn
[2024-01-24 13:41:00,526] [INFO] Running command: blastn -query GCF_003353055.1_ASM335305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/reference_markers.fasta -out GCF_003353055.1_ASM335305v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,621] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:01,621] [INFO] Target genome list was writen to GCF_003353055.1_ASM335305v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,629] [INFO] Task started: fastANI
[2024-01-24 13:41:01,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7484a9-69db-4e16-bba3-926cfc893662/GCF_003353055.1_ASM335305v1_genomic.fna.gz --refList GCF_003353055.1_ASM335305v1_genomic.fna/target_genomes.txt --output GCF_003353055.1_ASM335305v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:20,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:20,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:20,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:20,632] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:20,632] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:20,632] [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 lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	100.0	2931	2946	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	90.1248	1466	2946	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	90.0045	1539	2946	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	89.5605	1578	2946	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	89.5192	1617	2946	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	84.3146	1547	2946	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	81.5857	799	2946	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.2563	795	2946	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.1187	674	2946	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	77.8772	614	2946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:20,634] [INFO] DFAST Taxonomy check result was written to GCF_003353055.1_ASM335305v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:20,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:20,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:20,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/checkm_data
[2024-01-24 13:41:20,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:20,724] [INFO] Task started: CheckM
[2024-01-24 13:41:20,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003353055.1_ASM335305v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003353055.1_ASM335305v1_genomic.fna/checkm_input GCF_003353055.1_ASM335305v1_genomic.fna/checkm_result
[2024-01-24 13:42:43,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:43,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:43,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:43,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:43,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003353055.1_ASM335305v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:43,350] [INFO] Task started: Blastn
[2024-01-24 13:42:43,350] [INFO] Running command: blastn -query GCF_003353055.1_ASM335305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f59c45-644e-481b-8250-bc26909c3b98/dqc_reference/reference_markers_gtdb.fasta -out GCF_003353055.1_ASM335305v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:45,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:45,529] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:45,530] [INFO] Target genome list was writen to GCF_003353055.1_ASM335305v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:45,542] [INFO] Task started: fastANI
[2024-01-24 13:42:45,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e7484a9-69db-4e16-bba3-926cfc893662/GCF_003353055.1_ASM335305v1_genomic.fna.gz --refList GCF_003353055.1_ASM335305v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003353055.1_ASM335305v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:13,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:13,309] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:13,309] [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_003353055.1	s__Cupriavidus lacunae	100.0	2931	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.34	96.34	0.71	0.71	2	conclusive
GCF_000219215.1	s__Cupriavidus necator	91.8377	1860	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.10	95.22	0.79	0.76	13	-
GCF_000379565.1	s__Cupriavidus sp000379565	91.3659	1719	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900249755.1	s__Cupriavidus taiwanensis_D	90.31	1466	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.80	98.80	0.92	0.92	2	-
GCF_001598055.1	s__Cupriavidus nantongensis	90.1047	1468	2946	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	89.9822	1541	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	89.6912	1604	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_000069785.1	s__Cupriavidus taiwanensis	89.5628	1577	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	89.5507	1613	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCA_000471925.1	s__Cupriavidus pickettii_A	88.9072	1764	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744095.1	s__Cupriavidus necator_A	88.8964	1894	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004768545.1	s__Cupriavidus oxalaticus_A	87.8859	1681	2946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.89	98.53	0.88	0.85	3	-
GCF_000812465.1	s__Cupriavidus sp000812465	87.4572	1819	2946	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 13:43:13,311] [INFO] GTDB search result was written to GCF_003353055.1_ASM335305v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:13,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:13,315] [INFO] DFAST_QC result json was written to GCF_003353055.1_ASM335305v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:13,315] [INFO] DFAST_QC completed!
[2024-01-24 13:43:13,315] [INFO] Total running time: 0h2m44s