[2024-01-24 14:47:06,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:06,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:06,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference
[2024-01-24 14:47:07,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:07,678] [INFO] Task started: Prodigal
[2024-01-24 14:47:07,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ca1df7a-ddc1-43ab-a532-52bf135a9e7d/GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/cds.fna -a GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:38,960] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:38,960] [INFO] Task started: HMMsearch
[2024-01-24 14:47:38,960] [INFO] Running command: hmmsearch --tblout GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/reference_markers.hmm GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:39,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:39,556] [INFO] Found 6/6 markers.
[2024-01-24 14:47:39,633] [INFO] Query marker FASTA was written to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:39,633] [INFO] Task started: Blastn
[2024-01-24 14:47:39,634] [INFO] Running command: blastn -query GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/reference_markers.fasta -out GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:40,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:40,666] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:40,666] [INFO] Target genome list was writen to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:40,674] [INFO] Task started: fastANI
[2024-01-24 14:47:40,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca1df7a-ddc1-43ab-a532-52bf135a9e7d/GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna.gz --refList GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:07,599] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:07,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:07,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:07,609] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:48:07,610] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:48:07,610] [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
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	100.0	3241	3245	95	inconclusive
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	95.2393	2299	3245	95	inconclusive
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	93.9982	2349	3245	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	93.9831	2250	3245	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	90.7411	2077	3245	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	90.718	1970	3245	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.462	1957	3245	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	90.4331	1974	3245	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	90.2069	1957	3245	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.2339	1252	3245	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.8797	1470	3245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:07,611] [INFO] DFAST Taxonomy check result was written to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:48:07,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:07,612] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:07,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/checkm_data
[2024-01-24 14:48:07,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:07,705] [INFO] Task started: CheckM
[2024-01-24 14:48:07,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/checkm_input GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:49:34,218] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:34,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:34,257] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:34,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:34,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:49:34,259] [INFO] Task started: Blastn
[2024-01-24 14:49:34,259] [INFO] Running command: blastn -query GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f5a9ab1-9c06-4c9b-8193-9c58940ece3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:36,197] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:36,217] [INFO] Selected 10 target genomes.
[2024-01-24 14:49:36,217] [INFO] Target genome list was writen to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:36,233] [INFO] Task started: fastANI
[2024-01-24 14:49:36,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca1df7a-ddc1-43ab-a532-52bf135a9e7d/GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna.gz --refList GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:04,343] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:04,354] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:04,354] [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_900116445.1	s__Paraburkholderia aspalathi	100.0	3241	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	conclusive
GCF_902859805.1	s__Paraburkholderia sediminicola	94.0136	2347	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	93.9899	2249	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_900230185.1	s__Paraburkholderia sp900230185	93.566	2382	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	90.7492	2076	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	90.7061	1971	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	90.4264	1977	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	90.3027	2101	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_905220975.1	s__Paraburkholderia sp905220975	90.2225	1955	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610895.1	s__Paraburkholderia fungorum_B	89.3236	1979	3245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:04,356] [INFO] GTDB search result was written to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:04,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:04,361] [INFO] DFAST_QC result json was written to GCF_900116445.1_IMG-taxon_2671180117_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:50:04,362] [INFO] DFAST_QC completed!
[2024-01-24 14:50:04,362] [INFO] Total running time: 0h2m58s