[2024-01-24 13:37:25,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference
[2024-01-24 13:37:27,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,173] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg944f3105-3c68-4eab-84fc-642093c6910d/GCF_000163455.1_ASM16345v1_genomic.fna.gz | prodigal -d GCF_000163455.1_ASM16345v1_genomic.fna/cds.fna -a GCF_000163455.1_ASM16345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:39,942] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:39,943] [INFO] Task started: HMMsearch
[2024-01-24 13:37:39,943] [INFO] Running command: hmmsearch --tblout GCF_000163455.1_ASM16345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/reference_markers.hmm GCF_000163455.1_ASM16345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:40,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:40,284] [INFO] Found 6/6 markers.
[2024-01-24 13:37:40,326] [INFO] Query marker FASTA was written to GCF_000163455.1_ASM16345v1_genomic.fna/markers.fasta
[2024-01-24 13:37:40,326] [INFO] Task started: Blastn
[2024-01-24 13:37:40,326] [INFO] Running command: blastn -query GCF_000163455.1_ASM16345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/reference_markers.fasta -out GCF_000163455.1_ASM16345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:41,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:41,129] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:41,129] [INFO] Target genome list was writen to GCF_000163455.1_ASM16345v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:41,133] [INFO] Task started: fastANI
[2024-01-24 13:37:41,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg944f3105-3c68-4eab-84fc-642093c6910d/GCF_000163455.1_ASM16345v1_genomic.fna.gz --refList GCF_000163455.1_ASM16345v1_genomic.fna/target_genomes.txt --output GCF_000163455.1_ASM16345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:57,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:57,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:57,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:57,439] [INFO] Found 14 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:37:57,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:57,439] [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 pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	99.9977	1782	1795	95	conclusive
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	98.7474	1563	1795	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	98.7408	1514	1795	95	conclusive
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	98.6797	1574	1795	95	conclusive
Klebsiella pneumoniae	strain=FDAARGOS_775	GCA_006364295.1	573	573	type	True	98.6791	1563	1795	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=DSM 30104	GCA_000281755.1	72407	573	type	True	98.679	1561	1795	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	98.5503	1566	1795	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.9023	913	1795	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8212	916	1795	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7775	892	1795	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.6853	886	1795	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.4424	922	1795	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.0759	801	1795	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	81.0286	817	1795	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:57,441] [INFO] DFAST Taxonomy check result was written to GCF_000163455.1_ASM16345v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:57,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:57,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:57,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/checkm_data
[2024-01-24 13:37:57,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:57,493] [INFO] Task started: CheckM
[2024-01-24 13:37:57,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000163455.1_ASM16345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000163455.1_ASM16345v1_genomic.fna/checkm_input GCF_000163455.1_ASM16345v1_genomic.fna/checkm_result
[2024-01-24 13:38:33,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:33,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:33,967] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:33,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:33,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000163455.1_ASM16345v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:33,967] [INFO] Task started: Blastn
[2024-01-24 13:38:33,967] [INFO] Running command: blastn -query GCF_000163455.1_ASM16345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg986fcea4-ce26-43a0-b964-bb2c9ae32e1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000163455.1_ASM16345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:35,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:35,054] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:35,054] [INFO] Target genome list was writen to GCF_000163455.1_ASM16345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:35,067] [INFO] Task started: fastANI
[2024-01-24 13:38:35,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg944f3105-3c68-4eab-84fc-642093c6910d/GCF_000163455.1_ASM16345v1_genomic.fna.gz --refList GCF_000163455.1_ASM16345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000163455.1_ASM16345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:47,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:47,083] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:47,083] [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_000742135.1	s__Klebsiella pneumoniae	98.7343	1564	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	conclusive
GCF_900978845.1	s__Klebsiella africana	95.0554	1493	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000828055.2	s__Klebsiella variicola	94.6025	1501	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	93.5808	1468	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_000215745.1	s__Klebsiella aerogenes	85.9384	1224	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCA_002211745.1	s__Kluyvera georgiana_A	81.9191	917	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_000025565.1	s__Enterobacter cloacae	81.5786	933	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
GCF_009363175.1	s__Citrobacter_A telavivensis	81.1096	845	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017348915.1	s__UBA7405 sp000755535	81.0677	816	1795	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,084] [INFO] GTDB search result was written to GCF_000163455.1_ASM16345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:47,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:47,088] [INFO] DFAST_QC result json was written to GCF_000163455.1_ASM16345v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:47,088] [INFO] DFAST_QC completed!
[2024-01-24 13:38:47,088] [INFO] Total running time: 0h1m21s