[2024-01-24 15:09:55,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference
[2024-01-24 15:09:58,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,161] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg02ffd599-64a4-4c57-b7d0-c0f47caff575/GCF_900445775.1_51726_B01_genomic.fna.gz | prodigal -d GCF_900445775.1_51726_B01_genomic.fna/cds.fna -a GCF_900445775.1_51726_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:11,982] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:11,982] [INFO] Task started: HMMsearch
[2024-01-24 15:10:11,983] [INFO] Running command: hmmsearch --tblout GCF_900445775.1_51726_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/reference_markers.hmm GCF_900445775.1_51726_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:12,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:12,356] [INFO] Found 6/6 markers.
[2024-01-24 15:10:12,393] [INFO] Query marker FASTA was written to GCF_900445775.1_51726_B01_genomic.fna/markers.fasta
[2024-01-24 15:10:12,394] [INFO] Task started: Blastn
[2024-01-24 15:10:12,394] [INFO] Running command: blastn -query GCF_900445775.1_51726_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/reference_markers.fasta -out GCF_900445775.1_51726_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:13,366] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:13,371] [INFO] Selected 10 target genomes.
[2024-01-24 15:10:13,372] [INFO] Target genome list was writen to GCF_900445775.1_51726_B01_genomic.fna/target_genomes.txt
[2024-01-24 15:10:13,377] [INFO] Task started: fastANI
[2024-01-24 15:10:13,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg02ffd599-64a4-4c57-b7d0-c0f47caff575/GCF_900445775.1_51726_B01_genomic.fna.gz --refList GCF_900445775.1_51726_B01_genomic.fna/target_genomes.txt --output GCF_900445775.1_51726_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:32,641] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:32,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:32,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:32,656] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:32,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:32,656] [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
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	100.0	1249	1257	95	conclusive
Bordetella holmesii	strain=FDAARGOS_1539	GCA_020735985.1	35814	35814	type	True	99.9978	1228	1257	95	conclusive
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	83.4345	907	1257	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	83.4184	928	1257	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	83.408	905	1257	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	80.5851	586	1257	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	80.053	611	1257	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	79.4752	586	1257	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	77.9643	264	1257	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.0572	150	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:32,658] [INFO] DFAST Taxonomy check result was written to GCF_900445775.1_51726_B01_genomic.fna/tc_result.tsv
[2024-01-24 15:10:32,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:32,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:32,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/checkm_data
[2024-01-24 15:10:32,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:32,704] [INFO] Task started: CheckM
[2024-01-24 15:10:32,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445775.1_51726_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445775.1_51726_B01_genomic.fna/checkm_input GCF_900445775.1_51726_B01_genomic.fna/checkm_result
[2024-01-24 15:11:13,095] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:13,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,127] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:13,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:13,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445775.1_51726_B01_genomic.fna/markers.fasta)
[2024-01-24 15:11:13,128] [INFO] Task started: Blastn
[2024-01-24 15:11:13,128] [INFO] Running command: blastn -query GCF_900445775.1_51726_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e8bef9a-4ef0-45cc-8320-bd73b9cc06c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445775.1_51726_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:14,861] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:14,865] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:14,866] [INFO] Target genome list was writen to GCF_900445775.1_51726_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:14,876] [INFO] Task started: fastANI
[2024-01-24 15:11:14,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg02ffd599-64a4-4c57-b7d0-c0f47caff575/GCF_900445775.1_51726_B01_genomic.fna.gz --refList GCF_900445775.1_51726_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445775.1_51726_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:30,712] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:30,720] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:30,721] [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
GCA_000612485.1	s__Bordetella holmesii	99.9816	1229	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.96	99.94	1.00	0.99	92	conclusive
GCF_002261355.1	s__Bordetella sp002261355	85.1554	996	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000657795.2	s__Bordetella pseudohinzii	83.4514	905	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_001548475.1	s__Bordetella hinzii	83.4159	904	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_000306945.1	s__Bordetella pertussis	81.0614	582	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_900445835.1	s__Bordetella avium	80.8546	617	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	-
GCF_900078335.1	s__Bordetella trematum	80.6226	619	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,728] [INFO] GTDB search result was written to GCF_900445775.1_51726_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:30,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:30,737] [INFO] DFAST_QC result json was written to GCF_900445775.1_51726_B01_genomic.fna/dqc_result.json
[2024-01-24 15:11:30,737] [INFO] DFAST_QC completed!
[2024-01-24 15:11:30,737] [INFO] Total running time: 0h1m35s