[2024-01-24 11:59:35,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,260] [INFO] DQC Reference Directory: /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference
[2024-01-24 11:59:36,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,476] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,476] [INFO] Running command: gunzip -c /var/lib/cwl/stgdac011e2-f917-4b62-8bb2-17c6df1c985f/GCF_014489845.1_ASM1448984v1_genomic.fna.gz | prodigal -d GCF_014489845.1_ASM1448984v1_genomic.fna/cds.fna -a GCF_014489845.1_ASM1448984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:41,237] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:41,238] [INFO] Task started: HMMsearch
[2024-01-24 11:59:41,238] [INFO] Running command: hmmsearch --tblout GCF_014489845.1_ASM1448984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/reference_markers.hmm GCF_014489845.1_ASM1448984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:41,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:41,545] [INFO] Found 6/6 markers.
[2024-01-24 11:59:41,569] [INFO] Query marker FASTA was written to GCF_014489845.1_ASM1448984v1_genomic.fna/markers.fasta
[2024-01-24 11:59:41,570] [INFO] Task started: Blastn
[2024-01-24 11:59:41,570] [INFO] Running command: blastn -query GCF_014489845.1_ASM1448984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/reference_markers.fasta -out GCF_014489845.1_ASM1448984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:42,208] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:42,211] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:42,212] [INFO] Target genome list was writen to GCF_014489845.1_ASM1448984v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:42,289] [INFO] Task started: fastANI
[2024-01-24 11:59:42,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac011e2-f917-4b62-8bb2-17c6df1c985f/GCF_014489845.1_ASM1448984v1_genomic.fna.gz --refList GCF_014489845.1_ASM1448984v1_genomic.fna/target_genomes.txt --output GCF_014489845.1_ASM1448984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:49,625] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:49,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:49,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:49,636] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:49,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:49,637] [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 japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	100.0	865	867	95	conclusive
Frischella perrara	strain=PEB0191	GCA_000807275.1	1267021	1267021	type	True	79.5788	378	867	95	below_threshold
Frischella perrara	strain=DSM 104328	GCA_003182045.1	1267021	1267021	type	True	79.4406	386	867	95	below_threshold
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	78.1872	200	867	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	78.1399	192	867	95	below_threshold
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	78.1126	199	867	95	below_threshold
Orbus hercynius	strain=DSM 22228	GCA_003634275.1	593135	593135	type	True	78.0088	174	867	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	77.9977	175	867	95	below_threshold
Gallibacterium salpingitidis	strain=F150	GCA_001678495.1	505341	505341	type	True	76.2745	53	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:49,638] [INFO] DFAST Taxonomy check result was written to GCF_014489845.1_ASM1448984v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:49,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:49,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:49,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/checkm_data
[2024-01-24 11:59:49,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:49,666] [INFO] Task started: CheckM
[2024-01-24 11:59:49,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014489845.1_ASM1448984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014489845.1_ASM1448984v1_genomic.fna/checkm_input GCF_014489845.1_ASM1448984v1_genomic.fna/checkm_result
[2024-01-24 12:00:11,595] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:11,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:11,622] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:11,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:11,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014489845.1_ASM1448984v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:11,624] [INFO] Task started: Blastn
[2024-01-24 12:00:11,624] [INFO] Running command: blastn -query GCF_014489845.1_ASM1448984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9779e11-9e67-455e-8965-27e9133ccfdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014489845.1_ASM1448984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:12,446] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:12,450] [INFO] Selected 19 target genomes.
[2024-01-24 12:00:12,450] [INFO] Target genome list was writen to GCF_014489845.1_ASM1448984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:12,487] [INFO] Task started: fastANI
[2024-01-24 12:00:12,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac011e2-f917-4b62-8bb2-17c6df1c985f/GCF_014489845.1_ASM1448984v1_genomic.fna.gz --refList GCF_014489845.1_ASM1448984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014489845.1_ASM1448984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:21,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:21,128] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:21,128] [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_014489845.1	s__Frischella japonica	100.0	865	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Frischella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001693745.1	s__Gilliamella apicola_E	80.0584	208	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_000807275.1	s__Frischella perrara	79.5788	378	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Frischella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_001690185.1	s__Gilliamella apicola_I	79.1182	188	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693755.1	s__Gilliamella apicola_F	79.0541	179	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.98	98.98	0.93	0.93	2	-
GCF_001690595.1	s__Gilliamella apicola_M	78.4278	189	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690355.1	s__Gilliamella apicola_A	78.2518	144	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.35	99.00	0.94	0.93	5	-
GCF_000599985.1	s__Gilliamella apicola	78.1932	199	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.05	97.62	0.94	0.91	21	-
GCF_009795805.1	s__Gilliamella sp009795805	78.1882	189	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.74	98.02	0.90	0.84	5	-
GCF_001690655.1	s__Gilliamella apicola_P	78.1354	163	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202775.1	s__Gilliamella apis_A	78.1146	192	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.23	95.38	0.94	0.89	9	-
GCF_003634275.1	s__Orbus hercynius	78.0421	173	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Orbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002142155.1	s__Gilliamella apis	77.983	192	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.52	97.64	0.94	0.89	26	-
GCF_002142215.1	s__Gilliamella sp002142215	77.9432	189	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.95	96.09	0.93	0.88	3	-
GCF_900103255.1	s__Gilliamella bombi	77.8524	167	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.07	95.43	0.85	0.80	12	-
GCF_001693435.1	s__Gilliamella apicola_N	77.8371	205	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.54	96.32	0.92	0.89	19	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:21,130] [INFO] GTDB search result was written to GCF_014489845.1_ASM1448984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:21,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:21,138] [INFO] DFAST_QC result json was written to GCF_014489845.1_ASM1448984v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:21,138] [INFO] DFAST_QC completed!
[2024-01-24 12:00:21,138] [INFO] Total running time: 0h0m46s