[2024-01-24 12:21:43,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference
[2024-01-24 12:21:44,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:44,809] [INFO] Task started: Prodigal
[2024-01-24 12:21:44,809] [INFO] Running command: gunzip -c /var/lib/cwl/stgd045050e-8e07-4d3e-8b0f-0015ebd786d7/GCF_009712425.2_ASM971242v2_genomic.fna.gz | prodigal -d GCF_009712425.2_ASM971242v2_genomic.fna/cds.fna -a GCF_009712425.2_ASM971242v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:56,248] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:56,248] [INFO] Task started: HMMsearch
[2024-01-24 12:21:56,248] [INFO] Running command: hmmsearch --tblout GCF_009712425.2_ASM971242v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/reference_markers.hmm GCF_009712425.2_ASM971242v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:56,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:56,545] [INFO] Found 6/6 markers.
[2024-01-24 12:21:56,578] [INFO] Query marker FASTA was written to GCF_009712425.2_ASM971242v2_genomic.fna/markers.fasta
[2024-01-24 12:21:56,579] [INFO] Task started: Blastn
[2024-01-24 12:21:56,579] [INFO] Running command: blastn -query GCF_009712425.2_ASM971242v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/reference_markers.fasta -out GCF_009712425.2_ASM971242v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:57,514] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:57,518] [INFO] Selected 9 target genomes.
[2024-01-24 12:21:57,519] [INFO] Target genome list was writen to GCF_009712425.2_ASM971242v2_genomic.fna/target_genomes.txt
[2024-01-24 12:21:57,523] [INFO] Task started: fastANI
[2024-01-24 12:21:57,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgd045050e-8e07-4d3e-8b0f-0015ebd786d7/GCF_009712425.2_ASM971242v2_genomic.fna.gz --refList GCF_009712425.2_ASM971242v2_genomic.fna/target_genomes.txt --output GCF_009712425.2_ASM971242v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:04,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:04,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:04,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:04,886] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:04,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:04,886] [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
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	100.0	1222	1222	95	conclusive
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	99.9995	1221	1222	95	conclusive
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	85.797	905	1222	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	85.772	859	1222	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	85.7242	910	1222	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	76.7948	72	1222	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.4251	96	1222	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.9542	81	1222	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.9002	86	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:04,889] [INFO] DFAST Taxonomy check result was written to GCF_009712425.2_ASM971242v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:04,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:04,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:04,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/checkm_data
[2024-01-24 12:22:04,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:04,929] [INFO] Task started: CheckM
[2024-01-24 12:22:04,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009712425.2_ASM971242v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009712425.2_ASM971242v2_genomic.fna/checkm_input GCF_009712425.2_ASM971242v2_genomic.fna/checkm_result
[2024-01-24 12:22:40,720] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:40,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:40,740] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:40,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:40,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009712425.2_ASM971242v2_genomic.fna/markers.fasta)
[2024-01-24 12:22:40,742] [INFO] Task started: Blastn
[2024-01-24 12:22:40,742] [INFO] Running command: blastn -query GCF_009712425.2_ASM971242v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ef30a14-fdf3-42ec-b5e0-ef1766dfc864/dqc_reference/reference_markers_gtdb.fasta -out GCF_009712425.2_ASM971242v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:42,422] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:42,426] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:42,426] [INFO] Target genome list was writen to GCF_009712425.2_ASM971242v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:42,438] [INFO] Task started: fastANI
[2024-01-24 12:22:42,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgd045050e-8e07-4d3e-8b0f-0015ebd786d7/GCF_009712425.2_ASM971242v2_genomic.fna.gz --refList GCF_009712425.2_ASM971242v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009712425.2_ASM971242v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:52,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:52,920] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:52,921] [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_009712425.2	s__Aquisalinus luteolus	100.0	1222	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014640095.1	s__Aquisalinus flavus	85.797	905	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199615.1	s__Parvularcula dongshanensis	77.4591	153	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	77.4302	234	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	77.2965	163	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651915.1	s__Parvularcula lutaonensis	77.1353	149	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	77.0928	184	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848855.1	s__Pyruvatibacter mobilis	76.8692	101	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002943565.1	s__Marinicaulis flavus	76.8669	194	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	76.8325	162	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016742175.1	s__Aliihoeflea sp016742175	76.6924	125	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	76.5942	103	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	76.545	123	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.5178	112	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521215.1	s__Roseibium sp000521215	76.2301	53	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:52,922] [INFO] GTDB search result was written to GCF_009712425.2_ASM971242v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:52,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:52,927] [INFO] DFAST_QC result json was written to GCF_009712425.2_ASM971242v2_genomic.fna/dqc_result.json
[2024-01-24 12:22:52,927] [INFO] DFAST_QC completed!
[2024-01-24 12:22:52,927] [INFO] Total running time: 0h1m10s