[2024-01-24 12:37:09,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference
[2024-01-24 12:37:11,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,041] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,041] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbaf5e23-652c-4b96-a1ed-5339b20191f5/GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/cds.fna -a GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:25,219] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:25,220] [INFO] Task started: HMMsearch
[2024-01-24 12:37:25,220] [INFO] Running command: hmmsearch --tblout GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/reference_markers.hmm GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:25,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:25,532] [INFO] Found 6/6 markers.
[2024-01-24 12:37:25,579] [INFO] Query marker FASTA was written to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:37:25,579] [INFO] Task started: Blastn
[2024-01-24 12:37:25,580] [INFO] Running command: blastn -query GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/reference_markers.fasta -out GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:26,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:26,478] [INFO] Selected 16 target genomes.
[2024-01-24 12:37:26,479] [INFO] Target genome list was writen to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:37:26,485] [INFO] Task started: fastANI
[2024-01-24 12:37:26,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbaf5e23-652c-4b96-a1ed-5339b20191f5/GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna.gz --refList GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:43,666] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:43,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:43,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:43,681] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:43,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:43,681] [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
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	100.0	1701	1701	95	conclusive
Kosakonia oryziphila	strain=REICA_142	GCA_900094795.1	1005667	1005667	type	True	93.3616	1299	1701	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	92.6946	1430	1701	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	92.6797	1432	1701	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	84.309	1168	1701	95	below_threshold
Kosakonia oryzendophytica	strain=REICA_082	GCA_900094925.1	1005665	1005665	type	True	83.2862	1157	1701	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	82.6338	1050	1701	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.8596	833	1701	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.8421	802	1701	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.8277	833	1701	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	80.7415	868	1701	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.6647	825	1701	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	80.3264	795	1701	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	80.2887	780	1701	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	80.2592	767	1701	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	80.2556	773	1701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:43,683] [INFO] DFAST Taxonomy check result was written to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:37:43,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:43,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:43,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/checkm_data
[2024-01-24 12:37:43,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:43,736] [INFO] Task started: CheckM
[2024-01-24 12:37:43,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/checkm_input GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:38:27,519] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:27,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:27,541] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:27,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:27,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:38:27,543] [INFO] Task started: Blastn
[2024-01-24 12:38:27,543] [INFO] Running command: blastn -query GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf08204d7-cc8c-40a8-b0d4-6f32c32c6bb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:28,903] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:28,907] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:28,907] [INFO] Target genome list was writen to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:28,915] [INFO] Task started: fastANI
[2024-01-24 12:38:28,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbaf5e23-652c-4b96-a1ed-5339b20191f5/GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna.gz --refList GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:40,143] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:40,158] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:40,158] [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_900116535.1	s__Kosakonia arachidis	100.0	1701	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_018261615.1	s__Kosakonia sp018261615	93.8676	1281	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094795.1	s__Kosakonia oryziphila	93.3616	1299	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900109485.1	s__Kosakonia sacchari_B	92.9792	1420	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7228	98.05	98.05	0.93	0.93	2	-
GCF_000280495.2	s__Kosakonia radicincitans	92.896	1468	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_001658025.2	s__Kosakonia oryzae	92.6946	1430	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	98.47	96.95	0.97	0.93	3	-
GCF_002925905.1	s__Klebsiella michiganensis	80.3989	805	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCF_900200035.1	s__Klebsiella grimontii	80.3384	800	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_001598695.1	s__Klebsiella oxytoca	80.2594	774	1701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:40,160] [INFO] GTDB search result was written to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:40,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:40,164] [INFO] DFAST_QC result json was written to GCF_900116535.1_IMG-taxon_2651870175_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:38:40,164] [INFO] DFAST_QC completed!
[2024-01-24 12:38:40,164] [INFO] Total running time: 0h1m30s