[2024-01-24 12:15:04,034] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,036] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference
[2024-01-24 12:15:05,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,313] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg1556d767-4bb3-49c5-9edf-993f150f52d0/GCF_020735985.1_ASM2073598v1_genomic.fna.gz | prodigal -d GCF_020735985.1_ASM2073598v1_genomic.fna/cds.fna -a GCF_020735985.1_ASM2073598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,144] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,144] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,144] [INFO] Running command: hmmsearch --tblout GCF_020735985.1_ASM2073598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/reference_markers.hmm GCF_020735985.1_ASM2073598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:18,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:18,447] [INFO] Found 6/6 markers.
[2024-01-24 12:15:18,496] [INFO] Query marker FASTA was written to GCF_020735985.1_ASM2073598v1_genomic.fna/markers.fasta
[2024-01-24 12:15:18,496] [INFO] Task started: Blastn
[2024-01-24 12:15:18,497] [INFO] Running command: blastn -query GCF_020735985.1_ASM2073598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/reference_markers.fasta -out GCF_020735985.1_ASM2073598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,462] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,467] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:19,468] [INFO] Target genome list was writen to GCF_020735985.1_ASM2073598v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:19,473] [INFO] Task started: fastANI
[2024-01-24 12:15:19,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg1556d767-4bb3-49c5-9edf-993f150f52d0/GCF_020735985.1_ASM2073598v1_genomic.fna.gz --refList GCF_020735985.1_ASM2073598v1_genomic.fna/target_genomes.txt --output GCF_020735985.1_ASM2073598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:37,479] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:37,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:37,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:37,493] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:37,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:37,494] [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=FDAARGOS_1539	GCA_020735985.1	35814	35814	type	True	100.0	1229	1229	95	conclusive
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	99.9976	1227	1229	95	conclusive
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	83.5699	888	1229	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	83.4298	940	1229	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	83.2674	917	1229	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	80.4043	585	1229	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	79.9834	629	1229	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	79.5673	590	1229	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	77.8582	274	1229	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.0589	143	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,495] [INFO] DFAST Taxonomy check result was written to GCF_020735985.1_ASM2073598v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:37,496] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:37,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:37,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/checkm_data
[2024-01-24 12:15:37,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:37,535] [INFO] Task started: CheckM
[2024-01-24 12:15:37,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020735985.1_ASM2073598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020735985.1_ASM2073598v1_genomic.fna/checkm_input GCF_020735985.1_ASM2073598v1_genomic.fna/checkm_result
[2024-01-24 12:16:16,729] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:16,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,752] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:16,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:16,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020735985.1_ASM2073598v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:16,753] [INFO] Task started: Blastn
[2024-01-24 12:16:16,754] [INFO] Running command: blastn -query GCF_020735985.1_ASM2073598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31280c17-f9e6-4a3c-85fd-909f9deb61ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_020735985.1_ASM2073598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:18,441] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:18,445] [INFO] Selected 7 target genomes.
[2024-01-24 12:16:18,445] [INFO] Target genome list was writen to GCF_020735985.1_ASM2073598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:18,450] [INFO] Task started: fastANI
[2024-01-24 12:16:18,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg1556d767-4bb3-49c5-9edf-993f150f52d0/GCF_020735985.1_ASM2073598v1_genomic.fna.gz --refList GCF_020735985.1_ASM2073598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020735985.1_ASM2073598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:32,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:32,451] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:32,452] [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	99.9747	1226	1229	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	85.0966	1014	1229	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	83.58	887	1229	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	83.2708	916	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_900445835.1	s__Bordetella avium	81.036	600	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	-
GCF_000306945.1	s__Bordetella pertussis	80.9549	568	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_900078335.1	s__Bordetella trematum	80.4622	632	1229	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 12:16:32,455] [INFO] GTDB search result was written to GCF_020735985.1_ASM2073598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:32,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:32,459] [INFO] DFAST_QC result json was written to GCF_020735985.1_ASM2073598v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:32,459] [INFO] DFAST_QC completed!
[2024-01-24 12:16:32,459] [INFO] Total running time: 0h1m28s