[2024-01-25 19:24:45,021] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference
[2024-01-25 19:24:48,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,246] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad2e300-be87-4440-b21c-d18ec6e32998/GCF_000599985.1_ASM59998v1_genomic.fna.gz | prodigal -d GCF_000599985.1_ASM59998v1_genomic.fna/cds.fna -a GCF_000599985.1_ASM59998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:53,275] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:53,275] [INFO] Task started: HMMsearch
[2024-01-25 19:24:53,275] [INFO] Running command: hmmsearch --tblout GCF_000599985.1_ASM59998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/reference_markers.hmm GCF_000599985.1_ASM59998v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:53,554] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:53,555] [INFO] Found 6/6 markers.
[2024-01-25 19:24:53,582] [INFO] Query marker FASTA was written to GCF_000599985.1_ASM59998v1_genomic.fna/markers.fasta
[2024-01-25 19:24:53,582] [INFO] Task started: Blastn
[2024-01-25 19:24:53,583] [INFO] Running command: blastn -query GCF_000599985.1_ASM59998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/reference_markers.fasta -out GCF_000599985.1_ASM59998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:55,549] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:55,553] [INFO] Selected 12 target genomes.
[2024-01-25 19:24:55,553] [INFO] Target genome list was writen to GCF_000599985.1_ASM59998v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:55,768] [INFO] Task started: fastANI
[2024-01-25 19:24:55,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad2e300-be87-4440-b21c-d18ec6e32998/GCF_000599985.1_ASM59998v1_genomic.fna.gz --refList GCF_000599985.1_ASM59998v1_genomic.fna/target_genomes.txt --output GCF_000599985.1_ASM59998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:03,725] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:03,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:03,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:03,732] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:03,732] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:03,732] [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
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	100.0	1046	1046	95	conclusive
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	99.9393	997	1046	95	conclusive
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	81.2722	508	1046	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	80.5004	464	1046	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	80.1804	443	1046	95	below_threshold
Frischella perrara	strain=DSM 104328	GCA_003182045.1	1267021	1267021	type	True	79.7539	207	1046	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	78.1486	214	1046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:03,733] [INFO] DFAST Taxonomy check result was written to GCF_000599985.1_ASM59998v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:03,733] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:03,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:03,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/checkm_data
[2024-01-25 19:25:03,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:03,765] [INFO] Task started: CheckM
[2024-01-25 19:25:03,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000599985.1_ASM59998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000599985.1_ASM59998v1_genomic.fna/checkm_input GCF_000599985.1_ASM59998v1_genomic.fna/checkm_result
[2024-01-25 19:25:24,831] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:24,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:24,853] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:24,853] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:24,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000599985.1_ASM59998v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:24,854] [INFO] Task started: Blastn
[2024-01-25 19:25:24,854] [INFO] Running command: blastn -query GCF_000599985.1_ASM59998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d5063d0-efc4-44c5-baac-97e52c27d267/dqc_reference/reference_markers_gtdb.fasta -out GCF_000599985.1_ASM59998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:25,871] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:25,875] [INFO] Selected 16 target genomes.
[2024-01-25 19:25:25,875] [INFO] Target genome list was writen to GCF_000599985.1_ASM59998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:25,904] [INFO] Task started: fastANI
[2024-01-25 19:25:25,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad2e300-be87-4440-b21c-d18ec6e32998/GCF_000599985.1_ASM59998v1_genomic.fna.gz --refList GCF_000599985.1_ASM59998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000599985.1_ASM59998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:36,016] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:36,026] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:36,026] [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_000599985.1	s__Gilliamella apicola	100.0	1046	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.05	97.62	0.94	0.91	21	conclusive
GCF_001693435.1	s__Gilliamella apicola_N	93.3321	855	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.54	96.32	0.92	0.89	19	-
GCF_003202915.1	s__Gilliamella apicola_Q	81.8781	582	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.60	95.60	0.89	0.89	2	-
GCF_002142155.1	s__Gilliamella apis	81.2899	507	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.52	97.64	0.94	0.89	26	-
GCF_003202775.1	s__Gilliamella apis_A	81.1848	523	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.23	95.38	0.94	0.89	9	-
GCF_001693745.1	s__Gilliamella apicola_E	80.8211	471	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_900094945.1	s__Gilliamella bombicola	80.4879	464	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.14	97.05	0.94	0.93	3	-
GCF_001693755.1	s__Gilliamella apicola_F	80.4549	513	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.98	98.98	0.93	0.93	2	-
GCF_009795885.1	s__Gilliamella sp009795885	80.4479	510	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690495.1	s__Gilliamella apicola_G	80.404	489	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.43	99.43	0.96	0.96	2	-
GCF_001690525.1	s__Gilliamella apicola_H	80.3876	471	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.50	95.50	0.87	0.87	2	-
GCF_001690275.1	s__Gilliamella apicola_C	80.2001	469	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.79	96.31	0.88	0.82	9	-
GCF_009795805.1	s__Gilliamella sp009795805	80.1026	479	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.74	98.02	0.90	0.84	5	-
GCF_009795845.1	s__Gilliamella sp009795845	79.9937	450	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001690185.1	s__Gilliamella apicola_I	79.6449	424	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690195.1	s__Gilliamella apicola_L	79.5855	477	1046	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:36,028] [INFO] GTDB search result was written to GCF_000599985.1_ASM59998v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:36,029] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:36,031] [INFO] DFAST_QC result json was written to GCF_000599985.1_ASM59998v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:36,031] [INFO] DFAST_QC completed!
[2024-01-25 19:25:36,032] [INFO] Total running time: 0h0m51s