[2024-01-24 12:52:51,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference
[2024-01-24 12:52:53,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,753] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg45b7daf8-9c6c-4416-aca1-985fd0764caf/GCF_902459655.1_LMG_31108_genomic.fna.gz | prodigal -d GCF_902459655.1_LMG_31108_genomic.fna/cds.fna -a GCF_902459655.1_LMG_31108_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:13,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:13,153] [INFO] Task started: HMMsearch
[2024-01-24 12:53:13,153] [INFO] Running command: hmmsearch --tblout GCF_902459655.1_LMG_31108_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/reference_markers.hmm GCF_902459655.1_LMG_31108_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:13,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:13,446] [INFO] Found 6/6 markers.
[2024-01-24 12:53:13,494] [INFO] Query marker FASTA was written to GCF_902459655.1_LMG_31108_genomic.fna/markers.fasta
[2024-01-24 12:53:13,495] [INFO] Task started: Blastn
[2024-01-24 12:53:13,495] [INFO] Running command: blastn -query GCF_902459655.1_LMG_31108_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/reference_markers.fasta -out GCF_902459655.1_LMG_31108_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:14,396] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:14,400] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:14,401] [INFO] Target genome list was writen to GCF_902459655.1_LMG_31108_genomic.fna/target_genomes.txt
[2024-01-24 12:53:14,422] [INFO] Task started: fastANI
[2024-01-24 12:53:14,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b7daf8-9c6c-4416-aca1-985fd0764caf/GCF_902459655.1_LMG_31108_genomic.fna.gz --refList GCF_902459655.1_LMG_31108_genomic.fna/target_genomes.txt --output GCF_902459655.1_LMG_31108_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:34,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:34,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:34,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:34,535] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:34,536] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:34,536] [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 anhela	strain=LMG 31108	GCA_902459655.1	2508295	2508295	type	True	100.0	1981	1983	95	conclusive
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	88.673	1529	1983	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	86.4567	1489	1983	95	below_threshold
Pandoraea faecigallinarum	strain=DSM 23572	GCA_001029105.3	656179	656179	type	True	86.3922	1381	1983	95	below_threshold
Pandoraea anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	86.3595	1463	1983	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	86.349	1439	1983	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	86.3394	1413	1983	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	86.1267	1463	1983	95	below_threshold
Pandoraea vervacti	strain=NS15	GCA_000934605.2	656178	656178	type	True	86.0891	1440	1983	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	84.9126	1307	1983	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.2788	442	1983	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.2141	554	1983	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.2141	552	1983	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.087	483	1983	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.0271	508	1983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:34,538] [INFO] DFAST Taxonomy check result was written to GCF_902459655.1_LMG_31108_genomic.fna/tc_result.tsv
[2024-01-24 12:53:34,539] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:34,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:34,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/checkm_data
[2024-01-24 12:53:34,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:34,595] [INFO] Task started: CheckM
[2024-01-24 12:53:34,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459655.1_LMG_31108_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459655.1_LMG_31108_genomic.fna/checkm_input GCF_902459655.1_LMG_31108_genomic.fna/checkm_result
[2024-01-24 12:54:32,075] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:32,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,102] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:32,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:32,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459655.1_LMG_31108_genomic.fna/markers.fasta)
[2024-01-24 12:54:32,105] [INFO] Task started: Blastn
[2024-01-24 12:54:32,105] [INFO] Running command: blastn -query GCF_902459655.1_LMG_31108_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea74501-3211-40f3-be9e-eb84ff58257e/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459655.1_LMG_31108_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:33,756] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:33,760] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:33,760] [INFO] Target genome list was writen to GCF_902459655.1_LMG_31108_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:33,787] [INFO] Task started: fastANI
[2024-01-24 12:54:33,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg45b7daf8-9c6c-4416-aca1-985fd0764caf/GCF_902459655.1_LMG_31108_genomic.fna.gz --refList GCF_902459655.1_LMG_31108_genomic.fna/target_genomes_gtdb.txt --output GCF_902459655.1_LMG_31108_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:48,840] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:48,856] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:48,856] [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_902459655.1	s__Pandoraea anhela	100.0	1981	1983	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_902459735.1	s__Pandoraea capi	88.6631	1531	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_902459565.1	s__Pandoraea aquatica	86.4647	1488	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029105.3	s__Pandoraea faecigallinarum	86.3838	1382	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459765.1	s__Pandoraea anapnoica	86.3595	1463	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459615.1	s__Pandoraea commovens	86.3465	1439	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972785.3	s__Pandoraea oxalativorans	86.3394	1413	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814845.2	s__Pandoraea sputorum	86.2243	1477	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_902459775.1	s__Pandoraea captiosa	86.1331	1462	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934605.2	s__Pandoraea vervacti	86.0939	1439	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	84.908	1308	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:48,858] [INFO] GTDB search result was written to GCF_902459655.1_LMG_31108_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:48,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:48,865] [INFO] DFAST_QC result json was written to GCF_902459655.1_LMG_31108_genomic.fna/dqc_result.json
[2024-01-24 12:54:48,866] [INFO] DFAST_QC completed!
[2024-01-24 12:54:48,866] [INFO] Total running time: 0h1m58s