[2024-01-24 13:21:47,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference
[2024-01-24 13:21:48,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,623] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c1d7313-d74b-4e9b-9de1-bdaa9dfdfa3a/GCF_008801405.1_ASM880140v1_genomic.fna.gz | prodigal -d GCF_008801405.1_ASM880140v1_genomic.fna/cds.fna -a GCF_008801405.1_ASM880140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,953] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,954] [INFO] Running command: hmmsearch --tblout GCF_008801405.1_ASM880140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/reference_markers.hmm GCF_008801405.1_ASM880140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:10,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:10,312] [INFO] Found 6/6 markers.
[2024-01-24 13:22:10,373] [INFO] Query marker FASTA was written to GCF_008801405.1_ASM880140v1_genomic.fna/markers.fasta
[2024-01-24 13:22:10,374] [INFO] Task started: Blastn
[2024-01-24 13:22:10,374] [INFO] Running command: blastn -query GCF_008801405.1_ASM880140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/reference_markers.fasta -out GCF_008801405.1_ASM880140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:11,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:11,372] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:11,372] [INFO] Target genome list was writen to GCF_008801405.1_ASM880140v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:11,379] [INFO] Task started: fastANI
[2024-01-24 13:22:11,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1d7313-d74b-4e9b-9de1-bdaa9dfdfa3a/GCF_008801405.1_ASM880140v1_genomic.fna.gz --refList GCF_008801405.1_ASM880140v1_genomic.fna/target_genomes.txt --output GCF_008801405.1_ASM880140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:26,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:26,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:26,865] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:26,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:26,865] [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
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	100.0	1899	1899	95	conclusive
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	87.0697	1305	1899	95	below_threshold
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	87.0257	1304	1899	95	below_threshold
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	86.9267	1282	1899	95	below_threshold
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	86.915	1284	1899	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	86.8465	1293	1899	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	86.6848	1246	1899	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	85.2448	1050	1899	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	85.2205	1067	1899	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.489	552	1899	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.3053	564	1899	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.0444	461	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,867] [INFO] DFAST Taxonomy check result was written to GCF_008801405.1_ASM880140v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:26,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:26,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:26,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/checkm_data
[2024-01-24 13:22:26,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,926] [INFO] Task started: CheckM
[2024-01-24 13:22:26,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801405.1_ASM880140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801405.1_ASM880140v1_genomic.fna/checkm_input GCF_008801405.1_ASM880140v1_genomic.fna/checkm_result
[2024-01-24 13:23:33,526] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:33,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:33,548] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:33,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:33,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801405.1_ASM880140v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:33,549] [INFO] Task started: Blastn
[2024-01-24 13:23:33,549] [INFO] Running command: blastn -query GCF_008801405.1_ASM880140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e20a6ac-dcc5-48ce-848c-69888e71c58a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801405.1_ASM880140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:35,306] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:35,310] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:35,310] [INFO] Target genome list was writen to GCF_008801405.1_ASM880140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:35,318] [INFO] Task started: fastANI
[2024-01-24 13:23:35,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1d7313-d74b-4e9b-9de1-bdaa9dfdfa3a/GCF_008801405.1_ASM880140v1_genomic.fna.gz --refList GCF_008801405.1_ASM880140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801405.1_ASM880140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:49,020] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:49,033] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:49,034] [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_008801405.1	s__Ralstonia insidiosa	100.0	1899	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.92	96.99	0.90	0.85	9	conclusive
GCF_001078575.1	s__Ralstonia sp001078575	94.1645	1558	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.81	99.41	0.97	0.93	9	-
GCF_016429285.1	s__Ralstonia sp016429285	91.6201	1393	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801955.1	s__Ralstonia sp000801955	90.3583	1538	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298975.1	s__Ralstonia sp002298975	87.4883	1265	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620465.1	s__Ralstonia sp000620465	87.2504	1363	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.59	96.59	0.94	0.94	2	-
GCF_003851545.1	s__Ralstonia sp003851545	87.2419	1211	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997035.1	s__Ralstonia sp007997035	87.1509	1258	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016466415.1	s__Ralstonia pickettii	87.0351	1303	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	-
GCF_900115545.1	s__Ralstonia sp900115545	86.9657	1367	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:49,036] [INFO] GTDB search result was written to GCF_008801405.1_ASM880140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:49,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:49,039] [INFO] DFAST_QC result json was written to GCF_008801405.1_ASM880140v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:49,040] [INFO] DFAST_QC completed!
[2024-01-24 13:23:49,040] [INFO] Total running time: 0h2m2s