[2024-01-24 12:23:51,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:51,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:51,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference
[2024-01-24 12:23:52,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,330] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,330] [INFO] Running command: gunzip -c /var/lib/cwl/stgc211ac06-6916-4e02-a198-5756d48be7b0/GCF_019048125.1_ASM1904812v1_genomic.fna.gz | prodigal -d GCF_019048125.1_ASM1904812v1_genomic.fna/cds.fna -a GCF_019048125.1_ASM1904812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:06,224] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:06,224] [INFO] Task started: HMMsearch
[2024-01-24 12:24:06,224] [INFO] Running command: hmmsearch --tblout GCF_019048125.1_ASM1904812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/reference_markers.hmm GCF_019048125.1_ASM1904812v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:06,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:06,532] [INFO] Found 6/6 markers.
[2024-01-24 12:24:06,583] [INFO] Query marker FASTA was written to GCF_019048125.1_ASM1904812v1_genomic.fna/markers.fasta
[2024-01-24 12:24:06,583] [INFO] Task started: Blastn
[2024-01-24 12:24:06,584] [INFO] Running command: blastn -query GCF_019048125.1_ASM1904812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/reference_markers.fasta -out GCF_019048125.1_ASM1904812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:07,535] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:07,544] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:07,545] [INFO] Target genome list was writen to GCF_019048125.1_ASM1904812v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:07,551] [INFO] Task started: fastANI
[2024-01-24 12:24:07,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgc211ac06-6916-4e02-a198-5756d48be7b0/GCF_019048125.1_ASM1904812v1_genomic.fna.gz --refList GCF_019048125.1_ASM1904812v1_genomic.fna/target_genomes.txt --output GCF_019048125.1_ASM1904812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:28,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:28,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:28,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:28,453] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:24:28,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:28,453] [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
Klebsiella aerogenes	strain=FDAARGOS 1442	GCA_019048125.1	548	548	type	True	100.0	1760	1760	95	conclusive
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	99.994	1755	1760	95	conclusive
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	86.4808	1226	1760	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	86.4183	1221	1760	95	below_threshold
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	86.3088	1213	1760	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	86.2335	1230	1760	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	86.1298	1210	1760	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	86.0877	1176	1760	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	86.0528	1239	1760	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	84.2863	1223	1760	95	below_threshold
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	84.208	1200	1760	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	84.107	1204	1760	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	84.0977	1198	1760	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	83.994	1209	1760	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.7089	867	1760	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.7064	906	1760	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.6136	880	1760	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.5301	881	1760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:28,455] [INFO] DFAST Taxonomy check result was written to GCF_019048125.1_ASM1904812v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:28,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:28,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:28,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/checkm_data
[2024-01-24 12:24:28,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:28,509] [INFO] Task started: CheckM
[2024-01-24 12:24:28,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048125.1_ASM1904812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048125.1_ASM1904812v1_genomic.fna/checkm_input GCF_019048125.1_ASM1904812v1_genomic.fna/checkm_result
[2024-01-24 12:25:11,330] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:11,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:11,357] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:11,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:11,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048125.1_ASM1904812v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:11,359] [INFO] Task started: Blastn
[2024-01-24 12:25:11,359] [INFO] Running command: blastn -query GCF_019048125.1_ASM1904812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90523d56-add8-48bc-a262-9887dfaa9bde/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048125.1_ASM1904812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:12,841] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:12,846] [INFO] Selected 14 target genomes.
[2024-01-24 12:25:12,846] [INFO] Target genome list was writen to GCF_019048125.1_ASM1904812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:12,856] [INFO] Task started: fastANI
[2024-01-24 12:25:12,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgc211ac06-6916-4e02-a198-5756d48be7b0/GCF_019048125.1_ASM1904812v1_genomic.fna.gz --refList GCF_019048125.1_ASM1904812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048125.1_ASM1904812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:30,010] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:30,027] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:30,027] [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_000215745.1	s__Klebsiella aerogenes	99.9936	1755	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	conclusive
GCF_000828055.2	s__Klebsiella variicola	86.4235	1221	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_900978845.1	s__Klebsiella africana	86.1755	1167	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000742135.1	s__Klebsiella pneumoniae	86.1298	1210	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	85.7233	1204	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_002925905.1	s__Klebsiella michiganensis	84.298	1225	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCF_009707385.1	s__Klebsiella oxytoca_C	84.1646	1154	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900200035.1	s__Klebsiella grimontii	84.1161	1202	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_014298075.1	s__Klebsiella sp003752615	84.0874	1178	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.02	98.38	0.93	0.91	5	-
GCF_001598695.1	s__Klebsiella oxytoca	83.9907	1210	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_902158555.1	s__Klebsiella spallanzanii	83.8564	1154	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_000735435.1	s__Klebsiella planticola	83.7525	1189	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCF_003261575.2	s__Klebsiella huaxiensis	83.6971	1166	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCA_900759445.1	s__Klebsiella sp900759445	83.0124	680	1760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:30,029] [INFO] GTDB search result was written to GCF_019048125.1_ASM1904812v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:30,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:30,033] [INFO] DFAST_QC result json was written to GCF_019048125.1_ASM1904812v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:30,034] [INFO] DFAST_QC completed!
[2024-01-24 12:25:30,034] [INFO] Total running time: 0h1m39s