[2024-01-24 13:49:13,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference
[2024-01-24 13:49:14,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,484] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,485] [INFO] Running command: gunzip -c /var/lib/cwl/stgccbd5d30-a38d-4c41-a883-df873e4444d1/GCF_003182045.1_ASM318204v1_genomic.fna.gz | prodigal -d GCF_003182045.1_ASM318204v1_genomic.fna/cds.fna -a GCF_003182045.1_ASM318204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:19,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:19,190] [INFO] Task started: HMMsearch
[2024-01-24 13:49:19,190] [INFO] Running command: hmmsearch --tblout GCF_003182045.1_ASM318204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/reference_markers.hmm GCF_003182045.1_ASM318204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:19,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:19,404] [INFO] Found 6/6 markers.
[2024-01-24 13:49:19,428] [INFO] Query marker FASTA was written to GCF_003182045.1_ASM318204v1_genomic.fna/markers.fasta
[2024-01-24 13:49:19,429] [INFO] Task started: Blastn
[2024-01-24 13:49:19,429] [INFO] Running command: blastn -query GCF_003182045.1_ASM318204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/reference_markers.fasta -out GCF_003182045.1_ASM318204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:20,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:20,145] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:20,145] [INFO] Target genome list was writen to GCF_003182045.1_ASM318204v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:20,182] [INFO] Task started: fastANI
[2024-01-24 13:49:20,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgccbd5d30-a38d-4c41-a883-df873e4444d1/GCF_003182045.1_ASM318204v1_genomic.fna.gz --refList GCF_003182045.1_ASM318204v1_genomic.fna/target_genomes.txt --output GCF_003182045.1_ASM318204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,882] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,892] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:27,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:27,893] [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
Frischella perrara	strain=DSM 104328	GCA_003182045.1	1267021	1267021	type	True	100.0	829	832	95	conclusive
Frischella perrara	strain=PEB0191	GCA_000807275.1	1267021	1267021	type	True	99.9977	831	832	95	conclusive
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	79.9819	190	832	95	below_threshold
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	79.8002	195	832	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	79.3451	376	832	95	below_threshold
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	78.9601	189	832	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	78.3968	152	832	95	below_threshold
Orbus hercynius	strain=DSM 22228	GCA_003634275.1	593135	593135	type	True	78.2558	167	832	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	77.9753	171	832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,895] [INFO] DFAST Taxonomy check result was written to GCF_003182045.1_ASM318204v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/checkm_data
[2024-01-24 13:49:27,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,926] [INFO] Task started: CheckM
[2024-01-24 13:49:27,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182045.1_ASM318204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182045.1_ASM318204v1_genomic.fna/checkm_input GCF_003182045.1_ASM318204v1_genomic.fna/checkm_result
[2024-01-24 13:49:49,229] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:49,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,250] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:49,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:49,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182045.1_ASM318204v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:49,251] [INFO] Task started: Blastn
[2024-01-24 13:49:49,251] [INFO] Running command: blastn -query GCF_003182045.1_ASM318204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133ece20-82fa-4639-b05a-9142d35e7017/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182045.1_ASM318204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,335] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:50,335] [INFO] Target genome list was writen to GCF_003182045.1_ASM318204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:50,347] [INFO] Task started: fastANI
[2024-01-24 13:49:50,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgccbd5d30-a38d-4c41-a883-df873e4444d1/GCF_003182045.1_ASM318204v1_genomic.fna.gz --refList GCF_003182045.1_ASM318204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182045.1_ASM318204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:58,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,395] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:58,396] [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_000807275.1	s__Frischella perrara	99.9977	831	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Frischella	95.0	99.14	98.29	0.96	0.92	3	conclusive
GCF_000599985.1	s__Gilliamella apicola	79.9984	189	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.05	97.62	0.94	0.91	21	-
GCF_014489845.1	s__Frischella japonica	79.3209	378	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Frischella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094945.1	s__Gilliamella bombicola	78.4258	152	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.14	97.05	0.94	0.93	3	-
GCF_001690655.1	s__Gilliamella apicola_P	78.3549	161	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103255.1	s__Gilliamella bombi	78.3057	168	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.07	95.43	0.85	0.80	12	-
GCF_009795845.1	s__Gilliamella sp009795845	78.2978	160	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.98	99.98	0.99	0.99	3	-
GCF_003634275.1	s__Orbus hercynius	78.2946	164	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Orbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693745.1	s__Gilliamella apicola_E	78.2369	164	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_001690355.1	s__Gilliamella apicola_A	78.2217	158	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.35	99.00	0.94	0.93	5	-
GCF_001690185.1	s__Gilliamella apicola_I	78.1469	174	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690595.1	s__Gilliamella apicola_M	78.0724	172	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690525.1	s__Gilliamella apicola_H	77.9694	171	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.50	95.50	0.87	0.87	2	-
GCF_001690195.1	s__Gilliamella apicola_L	77.9327	175	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874625.1	s__Providencia rettgeri_A	77.0685	52	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,397] [INFO] GTDB search result was written to GCF_003182045.1_ASM318204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:58,398] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:58,402] [INFO] DFAST_QC result json was written to GCF_003182045.1_ASM318204v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:58,402] [INFO] DFAST_QC completed!
[2024-01-24 13:49:58,402] [INFO] Total running time: 0h0m45s