[2024-01-24 13:02:03,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference
[2024-01-24 13:02:04,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:04,787] [INFO] Task started: Prodigal
[2024-01-24 13:02:04,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg8608db99-0d16-41c3-90dd-a0e7c2ec2461/GCF_000807275.1_ASM80727v1_genomic.fna.gz | prodigal -d GCF_000807275.1_ASM80727v1_genomic.fna/cds.fna -a GCF_000807275.1_ASM80727v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:09,620] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:09,621] [INFO] Task started: HMMsearch
[2024-01-24 13:02:09,621] [INFO] Running command: hmmsearch --tblout GCF_000807275.1_ASM80727v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/reference_markers.hmm GCF_000807275.1_ASM80727v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:09,907] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:09,909] [INFO] Found 6/6 markers.
[2024-01-24 13:02:09,937] [INFO] Query marker FASTA was written to GCF_000807275.1_ASM80727v1_genomic.fna/markers.fasta
[2024-01-24 13:02:09,937] [INFO] Task started: Blastn
[2024-01-24 13:02:09,937] [INFO] Running command: blastn -query GCF_000807275.1_ASM80727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/reference_markers.fasta -out GCF_000807275.1_ASM80727v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,639] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:10,640] [INFO] Target genome list was writen to GCF_000807275.1_ASM80727v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:10,645] [INFO] Task started: fastANI
[2024-01-24 13:02:10,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg8608db99-0d16-41c3-90dd-a0e7c2ec2461/GCF_000807275.1_ASM80727v1_genomic.fna.gz --refList GCF_000807275.1_ASM80727v1_genomic.fna/target_genomes.txt --output GCF_000807275.1_ASM80727v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:19,509] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:19,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:19,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:19,524] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:19,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:19,525] [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=PEB0191	GCA_000807275.1	1267021	1267021	type	True	100.0	897	897	95	conclusive
Frischella perrara	strain=DSM 104328	GCA_003182045.1	1267021	1267021	type	True	99.9563	830	897	95	conclusive
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	80.6836	217	897	95	below_threshold
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	79.8608	209	897	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	79.4039	394	897	95	below_threshold
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	79.0146	197	897	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	78.724	58	897	95	below_threshold
Orbus hercynius	strain=DSM 22228	GCA_003634275.1	593135	593135	type	True	78.5408	162	897	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	78.4818	157	897	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	78.1198	167	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,526] [INFO] DFAST Taxonomy check result was written to GCF_000807275.1_ASM80727v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:19,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:19,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:19,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/checkm_data
[2024-01-24 13:02:19,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:19,558] [INFO] Task started: CheckM
[2024-01-24 13:02:19,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000807275.1_ASM80727v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000807275.1_ASM80727v1_genomic.fna/checkm_input GCF_000807275.1_ASM80727v1_genomic.fna/checkm_result
[2024-01-24 13:02:41,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:41,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:41,251] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:41,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:41,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000807275.1_ASM80727v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:41,252] [INFO] Task started: Blastn
[2024-01-24 13:02:41,253] [INFO] Running command: blastn -query GCF_000807275.1_ASM80727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefab92db-dfa1-454b-bed3-9840d78e4c43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000807275.1_ASM80727v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:42,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:42,315] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:42,315] [INFO] Target genome list was writen to GCF_000807275.1_ASM80727v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:42,321] [INFO] Task started: fastANI
[2024-01-24 13:02:42,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg8608db99-0d16-41c3-90dd-a0e7c2ec2461/GCF_000807275.1_ASM80727v1_genomic.fna.gz --refList GCF_000807275.1_ASM80727v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000807275.1_ASM80727v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:50,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:50,171] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:50,171] [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	100.0	897	897	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	80.6833	218	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.05	97.62	0.94	0.91	21	-
GCF_010748935.1	s__Providencia vermicola_A	79.9539	52	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.27	99.19	0.95	0.94	4	-
GCF_014489845.1	s__Frischella japonica	79.4039	394	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Frischella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874625.1	s__Providencia rettgeri_A	79.1263	54	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
GCF_001690355.1	s__Gilliamella apicola_A	78.6941	154	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.35	99.00	0.94	0.93	5	-
GCF_001690525.1	s__Gilliamella apicola_H	78.5645	171	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.50	95.50	0.87	0.87	2	-
GCF_003634275.1	s__Orbus hercynius	78.5304	163	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Orbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094945.1	s__Gilliamella bombicola	78.4962	157	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.14	97.05	0.94	0.93	3	-
GCF_001690185.1	s__Gilliamella apicola_I	78.4851	166	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693745.1	s__Gilliamella apicola_E	78.4834	166	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_001690655.1	s__Gilliamella apicola_P	78.4314	168	897	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	78.4188	179	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009795845.1	s__Gilliamella sp009795845	78.3342	163	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001690195.1	s__Gilliamella apicola_L	78.2807	187	897	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	78.039	175	897	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.07	95.43	0.85	0.80	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:50,173] [INFO] GTDB search result was written to GCF_000807275.1_ASM80727v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:50,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:50,177] [INFO] DFAST_QC result json was written to GCF_000807275.1_ASM80727v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:50,177] [INFO] DFAST_QC completed!
[2024-01-24 13:02:50,177] [INFO] Total running time: 0h0m47s