[2024-01-24 12:47:05,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,100] [INFO] DQC Reference Directory: /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference
[2024-01-24 12:47:06,345] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,346] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg26afbd5b-08e9-4db7-89eb-3b1bedfbce4e/GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/cds.fna -a GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:26,082] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:26,083] [INFO] Task started: HMMsearch
[2024-01-24 12:47:26,083] [INFO] Running command: hmmsearch --tblout GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/reference_markers.hmm GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:26,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:26,373] [INFO] Found 6/6 markers.
[2024-01-24 12:47:26,420] [INFO] Query marker FASTA was written to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:26,420] [INFO] Task started: Blastn
[2024-01-24 12:47:26,420] [INFO] Running command: blastn -query GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/reference_markers.fasta -out GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:27,576] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:27,581] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:27,582] [INFO] Target genome list was writen to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:27,586] [INFO] Task started: fastANI
[2024-01-24 12:47:27,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg26afbd5b-08e9-4db7-89eb-3b1bedfbce4e/GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna.gz --refList GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:44,932] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:44,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:44,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:44,943] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:44,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:44,944] [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 alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	100.0	2022	2024	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	94.6786	1701	2024	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	94.3296	1748	2024	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	93.5996	1714	2024	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	89.9096	1545	2024	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	88.83	1503	2024	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	84.8038	1352	2024	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.7814	798	2024	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	78.5876	574	2024	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.5046	585	2024	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.9443	560	2024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:44,946] [INFO] DFAST Taxonomy check result was written to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:44,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:44,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:44,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/checkm_data
[2024-01-24 12:47:44,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:45,002] [INFO] Task started: CheckM
[2024-01-24 12:47:45,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/checkm_input GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:48,146] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:48,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:48,165] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:48,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:48,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:48,166] [INFO] Task started: Blastn
[2024-01-24 12:48:48,166] [INFO] Running command: blastn -query GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdff0f9c8-7ab7-4b75-9b17-e4d1096fd534/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:50,304] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:50,307] [INFO] Selected 7 target genomes.
[2024-01-24 12:48:50,308] [INFO] Target genome list was writen to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:50,313] [INFO] Task started: fastANI
[2024-01-24 12:48:50,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg26afbd5b-08e9-4db7-89eb-3b1bedfbce4e/GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna.gz --refList GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:02,833] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:02,840] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:02,840] [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_900094595.1	s__Cupriavidus alkaliphilus	100.0	2022	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	conclusive
GCF_001598055.1	s__Cupriavidus nantongensis	94.6787	1701	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	94.4871	1779	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	94.3352	1747	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCA_013361545.1	s__Cupriavidus sp013361545	94.1468	1162	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.00	99.00	0.84	0.84	2	-
GCF_900250115.1	s__Cupriavidus taiwanensis_B	94.1353	1767	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.46	95.70	0.97	0.87	14	-
GCF_000069785.1	s__Cupriavidus taiwanensis	93.5884	1715	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:02,842] [INFO] GTDB search result was written to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:02,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:02,845] [INFO] DFAST_QC result json was written to GCF_900094595.1_IMG-taxon_2671180232_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:49:02,845] [INFO] DFAST_QC completed!
[2024-01-24 12:49:02,845] [INFO] Total running time: 0h1m58s