[2024-01-24 13:46:01,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,499] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference
[2024-01-24 13:46:02,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,725] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg26ca73b1-312b-4185-8146-385d77868bf9/GCF_902459645.1_LMG_31114_genomic.fna.gz | prodigal -d GCF_902459645.1_LMG_31114_genomic.fna/cds.fna -a GCF_902459645.1_LMG_31114_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:22,662] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:22,662] [INFO] Task started: HMMsearch
[2024-01-24 13:46:22,662] [INFO] Running command: hmmsearch --tblout GCF_902459645.1_LMG_31114_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/reference_markers.hmm GCF_902459645.1_LMG_31114_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:22,985] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:22,986] [INFO] Found 6/6 markers.
[2024-01-24 13:46:23,036] [INFO] Query marker FASTA was written to GCF_902459645.1_LMG_31114_genomic.fna/markers.fasta
[2024-01-24 13:46:23,036] [INFO] Task started: Blastn
[2024-01-24 13:46:23,036] [INFO] Running command: blastn -query GCF_902459645.1_LMG_31114_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/reference_markers.fasta -out GCF_902459645.1_LMG_31114_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,984] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:23,984] [INFO] Target genome list was writen to GCF_902459645.1_LMG_31114_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,991] [INFO] Task started: fastANI
[2024-01-24 13:46:23,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ca73b1-312b-4185-8146-385d77868bf9/GCF_902459645.1_LMG_31114_genomic.fna.gz --refList GCF_902459645.1_LMG_31114_genomic.fna/target_genomes.txt --output GCF_902459645.1_LMG_31114_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:45,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:45,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:45,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:45,422] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:45,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:45,423] [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
Pandoraea pneumonica	strain=LMG 31114	GCA_902459645.1	2508299	2508299	type	True	100.0	1942	1942	95	conclusive
Pandoraea iniqua	strain=LMG 31009	GCA_902459685.1	2508288	2508288	type	True	88.2428	1651	1942	95	below_threshold
Pandoraea norimbergensis	strain=DSM 11628	GCA_001465545.3	93219	93219	type	True	88.1747	1658	1942	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	84.1566	1412	1942	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.1445	1369	1942	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	84.1307	1260	1942	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	84.1169	1295	1942	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	84.1068	1385	1942	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	84.0831	1300	1942	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	83.7447	1181	1942	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	78.3413	575	1942	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.2681	526	1942	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.2499	551	1942	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.2176	539	1942	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.1167	541	1942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,424] [INFO] DFAST Taxonomy check result was written to GCF_902459645.1_LMG_31114_genomic.fna/tc_result.tsv
[2024-01-24 13:46:45,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:45,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:45,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/checkm_data
[2024-01-24 13:46:45,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:45,491] [INFO] Task started: CheckM
[2024-01-24 13:46:45,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459645.1_LMG_31114_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459645.1_LMG_31114_genomic.fna/checkm_input GCF_902459645.1_LMG_31114_genomic.fna/checkm_result
[2024-01-24 13:47:43,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:43,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:43,361] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:43,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:43,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459645.1_LMG_31114_genomic.fna/markers.fasta)
[2024-01-24 13:47:43,362] [INFO] Task started: Blastn
[2024-01-24 13:47:43,362] [INFO] Running command: blastn -query GCF_902459645.1_LMG_31114_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaf02c00-c183-4a1e-a3fb-fe9b4888fbbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459645.1_LMG_31114_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:45,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:45,109] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:45,110] [INFO] Target genome list was writen to GCF_902459645.1_LMG_31114_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:45,130] [INFO] Task started: fastANI
[2024-01-24 13:47:45,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ca73b1-312b-4185-8146-385d77868bf9/GCF_902459645.1_LMG_31114_genomic.fna.gz --refList GCF_902459645.1_LMG_31114_genomic.fna/target_genomes_gtdb.txt --output GCF_902459645.1_LMG_31114_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:57,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:57,567] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:57,567] [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_902459645.1	s__Pandoraea pneumonica	100.0	1942	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902459685.1	s__Pandoraea iniqua	88.2346	1652	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.87	97.87	0.92	0.92	2	-
GCF_002179965.1	s__Pandoraea sp002179965	88.196	1621	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_001465545.3	s__Pandoraea norimbergensis	88.184	1656	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459565.1	s__Pandoraea aquatica	84.1543	1412	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459735.1	s__Pandoraea capi	84.1407	1370	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_000815105.2	s__Pandoraea pulmonicola	84.1248	1295	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459615.1	s__Pandoraea commovens	84.1127	1384	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459665.1	s__Pandoraea cepalis	83.7467	1182	1942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:57,569] [INFO] GTDB search result was written to GCF_902459645.1_LMG_31114_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:57,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:57,573] [INFO] DFAST_QC result json was written to GCF_902459645.1_LMG_31114_genomic.fna/dqc_result.json
[2024-01-24 13:47:57,573] [INFO] DFAST_QC completed!
[2024-01-24 13:47:57,573] [INFO] Total running time: 0h1m56s