[2024-01-24 13:57:42,102] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,104] [INFO] DQC Reference Directory: /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference
[2024-01-24 13:57:43,402] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,402] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,403] [INFO] Running command: gunzip -c /var/lib/cwl/stge1ac7728-c72e-48fe-80e9-b8a6cc3f8456/GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna.gz | prodigal -d GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/cds.fna -a GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:12,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:12,105] [INFO] Task started: HMMsearch
[2024-01-24 13:58:12,105] [INFO] Running command: hmmsearch --tblout GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/reference_markers.hmm GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:12,534] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:12,535] [INFO] Found 6/6 markers.
[2024-01-24 13:58:12,624] [INFO] Query marker FASTA was written to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/markers.fasta
[2024-01-24 13:58:12,625] [INFO] Task started: Blastn
[2024-01-24 13:58:12,625] [INFO] Running command: blastn -query GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/reference_markers.fasta -out GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,774] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:13,774] [INFO] Target genome list was writen to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/target_genomes.txt
[2024-01-24 13:58:13,781] [INFO] Task started: fastANI
[2024-01-24 13:58:13,781] [INFO] Running command: fastANI --query /var/lib/cwl/stge1ac7728-c72e-48fe-80e9-b8a6cc3f8456/GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna.gz --refList GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/target_genomes.txt --output GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:48,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:48,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:48,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:48,641] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:48,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:48,642] [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
Caballeronia calidae		GCA_900044055.2	1777139	1777139	type	True	100.0	3035	3045	95	conclusive
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	89.3268	1680	3045	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	89.2562	1932	3045	95	below_threshold
Caballeronia catudaia		GCA_001544755.2	1777136	1777136	type	True	89.0903	1819	3045	95	below_threshold
Caballeronia arvi		GCA_001544695.2	1777135	1777135	type	True	89.0899	1992	3045	95	below_threshold
Caballeronia temeraria		GCA_001544795.2	1777137	1777137	type	True	89.0829	1836	3045	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	88.8678	1856	3045	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	88.8508	1794	3045	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	88.8311	1898	3045	95	below_threshold
Caballeronia ptereochthonis		GCA_001545075.2	1777144	1777144	type	True	88.7148	1757	3045	95	below_threshold
Caballeronia fortuita		GCA_001544835.2	1777138	1777138	type	True	88.6192	1708	3045	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.3778	1360	3045	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.2431	994	3045	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	80.7735	1015	3045	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.6681	1158	3045	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	80.0239	1055	3045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,644] [INFO] DFAST Taxonomy check result was written to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/tc_result.tsv
[2024-01-24 13:58:48,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:48,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:48,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/checkm_data
[2024-01-24 13:58:48,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:48,747] [INFO] Task started: CheckM
[2024-01-24 13:58:48,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/checkm_input GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/checkm_result
[2024-01-24 14:00:17,965] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:17,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:17,994] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:17,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:17,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/markers.fasta)
[2024-01-24 14:00:17,996] [INFO] Task started: Blastn
[2024-01-24 14:00:17,996] [INFO] Running command: blastn -query GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50c0c3b-803e-43e9-9832-45f16e23dc32/dqc_reference/reference_markers_gtdb.fasta -out GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:20,096] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:20,100] [INFO] Selected 13 target genomes.
[2024-01-24 14:00:20,100] [INFO] Target genome list was writen to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:20,115] [INFO] Task started: fastANI
[2024-01-24 14:00:20,116] [INFO] Running command: fastANI --query /var/lib/cwl/stge1ac7728-c72e-48fe-80e9-b8a6cc3f8456/GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna.gz --refList GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/target_genomes_gtdb.txt --output GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:48,009] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:48,021] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:48,021] [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_900044055.2	s__Caballeronia calidae	100.0	3035	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000648925.1	s__Caballeronia jiangsuensis	89.358	1853	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	96.41	96.41	0.81	0.81	2	-
GCF_900258035.1	s__Caballeronia novacaledonica	89.3496	1677	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544915.2	s__Caballeronia pedi	89.2541	1932	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408855.1	s__Caballeronia sp018408855	89.1972	1941	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.23	98.23	0.88	0.88	2	-
GCA_001580565.1	s__Caballeronia megalochromosomata	89.1243	1876	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544755.2	s__Caballeronia catudaia	89.086	1819	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544695.2	s__Caballeronia arvi	89.0674	1996	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544795.2	s__Caballeronia temeraria	89.0616	1839	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544575.2	s__Caballeronia cordobensis	88.8799	1854	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	98.18	97.54	0.94	0.91	5	-
GCF_000698575.1	s__Caballeronia zhejiangensis	88.8533	1794	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.44	99.18	0.93	0.92	4	-
GCF_001545075.1	s__Caballeronia ptereochthonis	88.7228	1756	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001189335.2	s__Caballeronia schumannianae_A	88.6102	550	3045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.68	95.68	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:48,027] [INFO] GTDB search result was written to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:48,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:48,033] [INFO] DFAST_QC result json was written to GCF_900044055.2_Burkholderia_sp._LMG_29321_genomic.fna/dqc_result.json
[2024-01-24 14:00:48,033] [INFO] DFAST_QC completed!
[2024-01-24 14:00:48,033] [INFO] Total running time: 0h3m6s