[2024-01-25 20:05:20,448] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,450] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,450] [INFO] DQC Reference Directory: /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference
[2024-01-25 20:05:21,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,587] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a10a134-73ea-4c46-9fb6-b595065a0368/GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna.gz | prodigal -d GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/cds.fna -a GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:51,721] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:51,721] [INFO] Task started: HMMsearch
[2024-01-25 20:05:51,721] [INFO] Running command: hmmsearch --tblout GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/reference_markers.hmm GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:52,139] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:52,140] [INFO] Found 6/6 markers.
[2024-01-25 20:05:52,216] [INFO] Query marker FASTA was written to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/markers.fasta
[2024-01-25 20:05:52,216] [INFO] Task started: Blastn
[2024-01-25 20:05:52,216] [INFO] Running command: blastn -query GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/reference_markers.fasta -out GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:53,074] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:53,077] [INFO] Selected 19 target genomes.
[2024-01-25 20:05:53,078] [INFO] Target genome list was writen to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/target_genomes.txt
[2024-01-25 20:05:53,090] [INFO] Task started: fastANI
[2024-01-25 20:05:53,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a10a134-73ea-4c46-9fb6-b595065a0368/GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna.gz --refList GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/target_genomes.txt --output GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:24,159] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:24,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:24,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:24,174] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:24,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:24,175] [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 udeis		GCA_001544555.2	1232866	1232866	type	True	100.0	3221	3228	95	conclusive
Caballeronia mineralivorans	strain=PML1(12)	GCA_001028175.1	2010198	2010198	type	True	87.6086	1962	3228	95	below_threshold
Caballeronia telluris		GCA_001544495.2	326475	326475	type	True	80.9135	1062	3228	95	below_threshold
Caballeronia choica		GCA_001544535.2	326476	326476	type	True	80.9122	1139	3228	95	below_threshold
Caballeronia humi		GCA_001544475.2	326474	326474	type	True	80.7191	1072	3228	95	below_threshold
Caballeronia arationis		GCA_001544975.2	1777142	1777142	type	True	80.6717	1099	3228	95	below_threshold
Caballeronia glathei	strain=DSM 50014	GCA_000698595.1	60547	60547	type	True	80.6714	1153	3228	95	below_threshold
Caballeronia glathei	strain=LMG 14190	GCA_000751215.2	60547	60547	type	True	80.6403	1155	3228	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	79.8487	1001	3228	95	below_threshold
Caballeronia zhejiangensis	strain=OP-1	GCA_000698575.1	871203	871203	type	True	79.8137	998	3228	95	below_threshold
Paraburkholderia sartisoli	strain=LMG 24000	GCA_900107685.1	83784	83784	type	True	79.7551	883	3228	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	79.7515	1043	3228	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	79.478	1004	3228	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	79.3626	981	3228	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	79.1367	930	3228	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	79.1084	986	3228	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.8977	752	3228	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.8929	768	3228	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	78.7018	820	3228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:24,176] [INFO] DFAST Taxonomy check result was written to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/tc_result.tsv
[2024-01-25 20:06:24,176] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:24,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:24,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/checkm_data
[2024-01-25 20:06:24,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:24,272] [INFO] Task started: CheckM
[2024-01-25 20:06:24,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/checkm_input GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/checkm_result
[2024-01-25 20:07:45,977] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:45,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:46,000] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:46,000] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:46,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/markers.fasta)
[2024-01-25 20:07:46,000] [INFO] Task started: Blastn
[2024-01-25 20:07:46,000] [INFO] Running command: blastn -query GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71e41b5-3ecd-4e23-b6f2-4545b4a4ca34/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:47,485] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:47,487] [INFO] Selected 8 target genomes.
[2024-01-25 20:07:47,488] [INFO] Target genome list was writen to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:47,495] [INFO] Task started: fastANI
[2024-01-25 20:07:47,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a10a134-73ea-4c46-9fb6-b595065a0368/GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna.gz --refList GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/target_genomes_gtdb.txt --output GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:03,801] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:03,807] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:03,807] [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_001544555.2	s__Caballeronia udeis	100.0	3221	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.62	95.53	0.77	0.76	8	conclusive
GCA_001190015.1	s__Caballeronia crenata	93.5946	538	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011493005.1	s__Caballeronia sp011493005	89.3713	1978	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.62	99.62	0.93	0.93	2	-
GCF_018449515.1	s__Caballeronia sp018449515	89.3417	1840	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220365.1	s__Caballeronia sordidicola_C	89.088	1975	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000729995.1	s__Caballeronia sordidicola_A	89.0687	2064	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766085.1	s__Caballeronia sp009766085	88.9351	1998	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449635.1	s__Caballeronia sp018449635	83.5434	1392	3228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:03,809] [INFO] GTDB search result was written to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:03,809] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:03,812] [INFO] DFAST_QC result json was written to GCF_001544555.2_Burkholderia_udeis_LMG_27134_genomic.fna/dqc_result.json
[2024-01-25 20:08:03,812] [INFO] DFAST_QC completed!
[2024-01-25 20:08:03,812] [INFO] Total running time: 0h2m43s