[2024-01-24 12:46:35,126] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference
[2024-01-24 12:46:36,270] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,270] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c97e3b9-b08a-4309-84e1-e4978c7522ec/GCF_009547075.1_ASM954707v1_genomic.fna.gz | prodigal -d GCF_009547075.1_ASM954707v1_genomic.fna/cds.fna -a GCF_009547075.1_ASM954707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:44,276] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:44,276] [INFO] Task started: HMMsearch
[2024-01-24 12:46:44,276] [INFO] Running command: hmmsearch --tblout GCF_009547075.1_ASM954707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/reference_markers.hmm GCF_009547075.1_ASM954707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:44,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:44,463] [INFO] Found 6/6 markers.
[2024-01-24 12:46:44,488] [INFO] Query marker FASTA was written to GCF_009547075.1_ASM954707v1_genomic.fna/markers.fasta
[2024-01-24 12:46:44,488] [INFO] Task started: Blastn
[2024-01-24 12:46:44,488] [INFO] Running command: blastn -query GCF_009547075.1_ASM954707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/reference_markers.fasta -out GCF_009547075.1_ASM954707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:45,202] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:45,205] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:45,206] [INFO] Target genome list was writen to GCF_009547075.1_ASM954707v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:45,221] [INFO] Task started: fastANI
[2024-01-24 12:46:45,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c97e3b9-b08a-4309-84e1-e4978c7522ec/GCF_009547075.1_ASM954707v1_genomic.fna.gz --refList GCF_009547075.1_ASM954707v1_genomic.fna/target_genomes.txt --output GCF_009547075.1_ASM954707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:53,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:53,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:53,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:53,532] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:53,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:53,532] [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
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	100.0	944	947	95	conclusive
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	92.5639	728	947	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	92.4556	776	947	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	92.3954	780	947	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	91.9559	785	947	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	91.8803	764	947	95	below_threshold
Gluconobacter kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	85.5295	658	947	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.6981	150	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:53,534] [INFO] DFAST Taxonomy check result was written to GCF_009547075.1_ASM954707v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:53,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:53,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:53,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/checkm_data
[2024-01-24 12:46:53,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:53,564] [INFO] Task started: CheckM
[2024-01-24 12:46:53,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009547075.1_ASM954707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009547075.1_ASM954707v1_genomic.fna/checkm_input GCF_009547075.1_ASM954707v1_genomic.fna/checkm_result
[2024-01-24 12:47:22,488] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:22,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:22,507] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:22,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:22,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009547075.1_ASM954707v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:22,508] [INFO] Task started: Blastn
[2024-01-24 12:47:22,508] [INFO] Running command: blastn -query GCF_009547075.1_ASM954707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64889327-879c-4d97-a267-9731fb81ffe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009547075.1_ASM954707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:23,607] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:23,611] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:23,611] [INFO] Target genome list was writen to GCF_009547075.1_ASM954707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:23,624] [INFO] Task started: fastANI
[2024-01-24 12:47:23,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c97e3b9-b08a-4309-84e1-e4978c7522ec/GCF_009547075.1_ASM954707v1_genomic.fna.gz --refList GCF_009547075.1_ASM954707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009547075.1_ASM954707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:32,373] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:32,383] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:32,383] [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_009547075.1	s__Gluconobacter sp009547075	100.0	944	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006539685.1	s__Gluconobacter oxydans	92.5639	728	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_001580675.1	s__Gluconobacter potus	91.9032	763	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_018811945.1	s__Gluconobacter sp018811945	91.7542	794	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539125.1	s__Gluconobacter sphaericus	89.5001	749	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
GCF_015244565.1	s__Gluconobacter vitians	89.0872	758	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	88.5706	727	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002723915.1	s__Gluconobacter albidus	86.906	728	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_007988905.1	s__Gluconobacter kanchanaburiensis	85.5295	658	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:32,385] [INFO] GTDB search result was written to GCF_009547075.1_ASM954707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:32,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:32,388] [INFO] DFAST_QC result json was written to GCF_009547075.1_ASM954707v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:32,388] [INFO] DFAST_QC completed!
[2024-01-24 12:47:32,388] [INFO] Total running time: 0h0m57s