[2024-01-24 13:13:35,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:35,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:35,780] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference
[2024-01-24 13:13:37,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:37,016] [INFO] Task started: Prodigal
[2024-01-24 13:13:37,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg778f68cd-fd84-4dac-8bee-1771454a414f/GCF_902459775.1_LMG_31118_genomic.fna.gz | prodigal -d GCF_902459775.1_LMG_31118_genomic.fna/cds.fna -a GCF_902459775.1_LMG_31118_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:58,136] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:58,136] [INFO] Task started: HMMsearch
[2024-01-24 13:13:58,136] [INFO] Running command: hmmsearch --tblout GCF_902459775.1_LMG_31118_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/reference_markers.hmm GCF_902459775.1_LMG_31118_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:58,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:58,442] [INFO] Found 6/6 markers.
[2024-01-24 13:13:58,490] [INFO] Query marker FASTA was written to GCF_902459775.1_LMG_31118_genomic.fna/markers.fasta
[2024-01-24 13:13:58,491] [INFO] Task started: Blastn
[2024-01-24 13:13:58,491] [INFO] Running command: blastn -query GCF_902459775.1_LMG_31118_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/reference_markers.fasta -out GCF_902459775.1_LMG_31118_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:59,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:59,432] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:59,432] [INFO] Target genome list was writen to GCF_902459775.1_LMG_31118_genomic.fna/target_genomes.txt
[2024-01-24 13:13:59,439] [INFO] Task started: fastANI
[2024-01-24 13:13:59,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg778f68cd-fd84-4dac-8bee-1771454a414f/GCF_902459775.1_LMG_31118_genomic.fna.gz --refList GCF_902459775.1_LMG_31118_genomic.fna/target_genomes.txt --output GCF_902459775.1_LMG_31118_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:20,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:20,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:20,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:20,424] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:20,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:20,425] [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 captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	100.0	2030	2030	95	conclusive
Pandoraea vervacti	strain=NS15	GCA_000934605.2	656178	656178	type	True	93.9745	1762	2030	95	below_threshold
Pandoraea faecigallinarum	strain=DSM 23572	GCA_001029105.3	656179	656179	type	True	86.7728	1492	2030	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	86.6784	1465	2030	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	86.2152	1480	2030	95	below_threshold
Pandoraea anhela	strain=LMG 31108	GCA_902459655.1	2508295	2508295	type	True	86.0607	1470	2030	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	86.021	1496	2030	95	below_threshold
Pandoraea anapnoica	strain=LMG 31117	GCA_902459765.1	2508301	2508301	type	True	86.017	1498	2030	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	85.9824	1491	2030	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	84.6684	1304	2030	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	84.2956	1294	2030	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.3313	420	2030	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.2543	554	2030	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.2439	546	2030	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.2415	547	2030	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	78.1379	472	2030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:20,426] [INFO] DFAST Taxonomy check result was written to GCF_902459775.1_LMG_31118_genomic.fna/tc_result.tsv
[2024-01-24 13:14:20,427] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:20,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:20,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/checkm_data
[2024-01-24 13:14:20,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:20,486] [INFO] Task started: CheckM
[2024-01-24 13:14:20,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459775.1_LMG_31118_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459775.1_LMG_31118_genomic.fna/checkm_input GCF_902459775.1_LMG_31118_genomic.fna/checkm_result
[2024-01-24 13:15:21,815] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:21,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:21,839] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:21,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:21,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459775.1_LMG_31118_genomic.fna/markers.fasta)
[2024-01-24 13:15:21,840] [INFO] Task started: Blastn
[2024-01-24 13:15:21,840] [INFO] Running command: blastn -query GCF_902459775.1_LMG_31118_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3d0056-e796-40cb-a71e-c8ea2537e102/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459775.1_LMG_31118_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:23,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:23,518] [INFO] Selected 11 target genomes.
[2024-01-24 13:15:23,518] [INFO] Target genome list was writen to GCF_902459775.1_LMG_31118_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:23,527] [INFO] Task started: fastANI
[2024-01-24 13:15:23,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg778f68cd-fd84-4dac-8bee-1771454a414f/GCF_902459775.1_LMG_31118_genomic.fna.gz --refList GCF_902459775.1_LMG_31118_genomic.fna/target_genomes_gtdb.txt --output GCF_902459775.1_LMG_31118_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:38,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:38,296] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:38,297] [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_902459775.1	s__Pandoraea captiosa	100.0	2030	2030	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_000934605.2	s__Pandoraea vervacti	93.9745	1762	2030	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	86.7876	1490	2030	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	86.6707	1467	2030	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	86.2267	1478	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459655.1	s__Pandoraea anhela	86.0517	1471	2030	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	86.0192	1498	2030	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	86.0149	1496	2030	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	85.9824	1491	2030	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	84.674	1303	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459585.1	s__Pandoraea nosoerga	84.2899	1295	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:38,299] [INFO] GTDB search result was written to GCF_902459775.1_LMG_31118_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:38,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:38,302] [INFO] DFAST_QC result json was written to GCF_902459775.1_LMG_31118_genomic.fna/dqc_result.json
[2024-01-24 13:15:38,303] [INFO] DFAST_QC completed!
[2024-01-24 13:15:38,303] [INFO] Total running time: 0h2m3s