[2024-01-24 12:37:23,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:23,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:23,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference
[2024-01-24 12:37:24,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:24,863] [INFO] Task started: Prodigal
[2024-01-24 12:37:24,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a24ef3a-3d3c-446a-8704-4470b278ab8c/GCF_001049515.1_Pandoraea_assembly_1_genomic.fna.gz | prodigal -d GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/cds.fna -a GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:42,849] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:42,849] [INFO] Task started: HMMsearch
[2024-01-24 12:37:42,849] [INFO] Running command: hmmsearch --tblout GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/reference_markers.hmm GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:43,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:43,154] [INFO] Found 6/6 markers.
[2024-01-24 12:37:43,197] [INFO] Query marker FASTA was written to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/markers.fasta
[2024-01-24 12:37:43,197] [INFO] Task started: Blastn
[2024-01-24 12:37:43,197] [INFO] Running command: blastn -query GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/reference_markers.fasta -out GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:43,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:43,996] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:43,997] [INFO] Target genome list was writen to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:44,002] [INFO] Task started: fastANI
[2024-01-24 12:37:44,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a24ef3a-3d3c-446a-8704-4470b278ab8c/GCF_001049515.1_Pandoraea_assembly_1_genomic.fna.gz --refList GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/target_genomes.txt --output GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:00,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:00,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:00,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:00,603] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:00,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:00,603] [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 apista	strain=LMG16407	GCA_001049515.1	93218	93218	type	True	100.0	1824	1828	95	conclusive
Pandoraea apista	strain=DSM 16535	GCA_001465595.2	93218	93218	type	True	99.9909	1824	1828	95	conclusive
Pandoraea fibrosis	strain=6399	GCA_000807775.2	1891094	1891094	type	True	89.8333	1529	1828	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	88.8489	1473	1828	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	88.8027	1424	1828	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	88.5468	1460	1828	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.475	517	1828	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.2425	412	1828	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.1374	470	1828	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.0012	479	1828	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	77.9837	526	1828	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.152	53	1828	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	75.6096	54	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:00,605] [INFO] DFAST Taxonomy check result was written to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:00,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:00,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:00,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/checkm_data
[2024-01-24 12:38:00,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:00,658] [INFO] Task started: CheckM
[2024-01-24 12:38:00,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/checkm_input GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/checkm_result
[2024-01-24 12:38:52,661] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:52,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:52,684] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:52,684] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:52,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 12:38:52,685] [INFO] Task started: Blastn
[2024-01-24 12:38:52,685] [INFO] Running command: blastn -query GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44ab78c2-bcc3-47f6-95e5-1ffad2b7ee07/dqc_reference/reference_markers_gtdb.fasta -out GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:53,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:53,941] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:53,941] [INFO] Target genome list was writen to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:53,951] [INFO] Task started: fastANI
[2024-01-24 12:38:53,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a24ef3a-3d3c-446a-8704-4470b278ab8c/GCF_001049515.1_Pandoraea_assembly_1_genomic.fna.gz --refList GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:04,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:04,720] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:04,721] [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_001465595.2	s__Pandoraea apista	99.9909	1824	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.24	99.05	0.93	0.91	21	conclusive
GCF_000807775.2	s__Pandoraea fibrosis	89.8259	1530	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_902459745.1	s__Pandoraea communis	88.8489	1473	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459805.1	s__Pandoraea bronchicola	88.799	1424	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459555.1	s__Pandoraea horticolens	88.5239	1463	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_902459735.1	s__Pandoraea capi	85.1023	1365	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_003206645.1	s__Salinicola aestuarinus	75.6096	54	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:04,722] [INFO] GTDB search result was written to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:04,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:04,726] [INFO] DFAST_QC result json was written to GCF_001049515.1_Pandoraea_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 12:39:04,726] [INFO] DFAST_QC completed!
[2024-01-24 12:39:04,726] [INFO] Total running time: 0h1m41s