[2024-01-25 18:14:05,896] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference
[2024-01-25 18:14:07,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:07,072] [INFO] Task started: Prodigal
[2024-01-25 18:14:07,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg145c66be-217b-4d1f-ba9a-d956a5ca3951/GCF_000067045.1_ASM6704v1_genomic.fna.gz | prodigal -d GCF_000067045.1_ASM6704v1_genomic.fna/cds.fna -a GCF_000067045.1_ASM6704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:17,658] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:17,659] [INFO] Task started: HMMsearch
[2024-01-25 18:14:17,659] [INFO] Running command: hmmsearch --tblout GCF_000067045.1_ASM6704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/reference_markers.hmm GCF_000067045.1_ASM6704v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:17,899] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:17,900] [INFO] Found 6/6 markers.
[2024-01-25 18:14:17,931] [INFO] Query marker FASTA was written to GCF_000067045.1_ASM6704v1_genomic.fna/markers.fasta
[2024-01-25 18:14:17,931] [INFO] Task started: Blastn
[2024-01-25 18:14:17,931] [INFO] Running command: blastn -query GCF_000067045.1_ASM6704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/reference_markers.fasta -out GCF_000067045.1_ASM6704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:18,812] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:18,814] [INFO] Selected 11 target genomes.
[2024-01-25 18:14:18,815] [INFO] Target genome list was writen to GCF_000067045.1_ASM6704v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:18,818] [INFO] Task started: fastANI
[2024-01-25 18:14:18,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg145c66be-217b-4d1f-ba9a-d956a5ca3951/GCF_000067045.1_ASM6704v1_genomic.fna.gz --refList GCF_000067045.1_ASM6704v1_genomic.fna/target_genomes.txt --output GCF_000067045.1_ASM6704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:29,564] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:29,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:29,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:29,573] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:14:29,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:29,573] [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
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	100.0	1328	1331	95	conclusive
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	99.1076	1113	1331	95	conclusive
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	99.1013	1172	1331	95	conclusive
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	83.4868	759	1331	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	82.9958	744	1331	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	82.941	734	1331	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.7327	357	1331	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.469	230	1331	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.673	172	1331	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.451	354	1331	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.1133	209	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:29,574] [INFO] DFAST Taxonomy check result was written to GCF_000067045.1_ASM6704v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:29,575] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:29,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:29,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/checkm_data
[2024-01-25 18:14:29,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:29,616] [INFO] Task started: CheckM
[2024-01-25 18:14:29,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000067045.1_ASM6704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000067045.1_ASM6704v1_genomic.fna/checkm_input GCF_000067045.1_ASM6704v1_genomic.fna/checkm_result
[2024-01-25 18:15:07,990] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:07,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:08,013] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:08,013] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:08,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000067045.1_ASM6704v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:08,014] [INFO] Task started: Blastn
[2024-01-25 18:15:08,014] [INFO] Running command: blastn -query GCF_000067045.1_ASM6704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5c5b72-6e86-40da-b177-8ea56e80546c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000067045.1_ASM6704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:09,668] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:09,672] [INFO] Selected 10 target genomes.
[2024-01-25 18:15:09,672] [INFO] Target genome list was writen to GCF_000067045.1_ASM6704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:09,679] [INFO] Task started: fastANI
[2024-01-25 18:15:09,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg145c66be-217b-4d1f-ba9a-d956a5ca3951/GCF_000067045.1_ASM6704v1_genomic.fna.gz --refList GCF_000067045.1_ASM6704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000067045.1_ASM6704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:19,939] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:19,946] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:19,946] [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_000021325.1	s__Gluconacetobacter diazotrophicus	99.1086	1170	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	conclusive
GCF_014174305.1	s__Gluconacetobacter johannae	84.3152	796	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	84.0898	811	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_014174375.1	s__Gluconacetobacter asukensis	84.0239	800	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	83.9972	778	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174155.1	s__Gluconacetobacter tumulisoli	83.9291	796	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174255.1	s__Gluconacetobacter sacchari	83.9248	786	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	83.6709	780	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	83.5992	761	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	83.4987	759	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:19,949] [INFO] GTDB search result was written to GCF_000067045.1_ASM6704v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:19,950] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:19,952] [INFO] DFAST_QC result json was written to GCF_000067045.1_ASM6704v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:19,953] [INFO] DFAST_QC completed!
[2024-01-25 18:15:19,953] [INFO] Total running time: 0h1m14s