[2024-01-25 17:44:05,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference
[2024-01-25 17:44:06,653] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,653] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,654] [INFO] Running command: gunzip -c /var/lib/cwl/stge30842ef-8725-43e4-ab24-b4c91958b4cc/GCF_900636985.1_45889_C01_genomic.fna.gz | prodigal -d GCF_900636985.1_45889_C01_genomic.fna/cds.fna -a GCF_900636985.1_45889_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:19,809] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:19,810] [INFO] Task started: HMMsearch
[2024-01-25 17:44:19,810] [INFO] Running command: hmmsearch --tblout GCF_900636985.1_45889_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/reference_markers.hmm GCF_900636985.1_45889_C01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:20,144] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:20,147] [INFO] Found 6/6 markers.
[2024-01-25 17:44:20,197] [INFO] Query marker FASTA was written to GCF_900636985.1_45889_C01_genomic.fna/markers.fasta
[2024-01-25 17:44:20,197] [INFO] Task started: Blastn
[2024-01-25 17:44:20,197] [INFO] Running command: blastn -query GCF_900636985.1_45889_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/reference_markers.fasta -out GCF_900636985.1_45889_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:20,980] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:20,983] [INFO] Selected 13 target genomes.
[2024-01-25 17:44:20,983] [INFO] Target genome list was writen to GCF_900636985.1_45889_C01_genomic.fna/target_genomes.txt
[2024-01-25 17:44:20,989] [INFO] Task started: fastANI
[2024-01-25 17:44:20,989] [INFO] Running command: fastANI --query /var/lib/cwl/stge30842ef-8725-43e4-ab24-b4c91958b4cc/GCF_900636985.1_45889_C01_genomic.fna.gz --refList GCF_900636985.1_45889_C01_genomic.fna/target_genomes.txt --output GCF_900636985.1_45889_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:37,556] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:37,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:37,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:37,565] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:44:37,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:37,565] [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 oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	100.0	1952	1952	95	conclusive
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	99.9856	1910	1952	95	conclusive
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	99.9831	1891	1952	95	conclusive
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	92.5093	1650	1952	95	below_threshold
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	92.4619	1624	1952	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	91.6943	1624	1952	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	84.1482	1309	1952	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	84.003	1291	1952	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	83.8488	1286	1952	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.7181	897	1952	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.6244	881	1952	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5125	966	1952	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.4113	895	1952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:37,566] [INFO] DFAST Taxonomy check result was written to GCF_900636985.1_45889_C01_genomic.fna/tc_result.tsv
[2024-01-25 17:44:37,567] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:37,567] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:37,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/checkm_data
[2024-01-25 17:44:37,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:37,623] [INFO] Task started: CheckM
[2024-01-25 17:44:37,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900636985.1_45889_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900636985.1_45889_C01_genomic.fna/checkm_input GCF_900636985.1_45889_C01_genomic.fna/checkm_result
[2024-01-25 17:45:17,799] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:17,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:17,818] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:17,819] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:17,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900636985.1_45889_C01_genomic.fna/markers.fasta)
[2024-01-25 17:45:17,819] [INFO] Task started: Blastn
[2024-01-25 17:45:17,819] [INFO] Running command: blastn -query GCF_900636985.1_45889_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6524d9e-95e6-41c4-bd9b-6eb2c9b2e12a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900636985.1_45889_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:18,941] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:18,943] [INFO] Selected 10 target genomes.
[2024-01-25 17:45:18,943] [INFO] Target genome list was writen to GCF_900636985.1_45889_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:18,953] [INFO] Task started: fastANI
[2024-01-25 17:45:18,954] [INFO] Running command: fastANI --query /var/lib/cwl/stge30842ef-8725-43e4-ab24-b4c91958b4cc/GCF_900636985.1_45889_C01_genomic.fna.gz --refList GCF_900636985.1_45889_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900636985.1_45889_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:33,295] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:33,301] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:33,302] [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_001598695.1	s__Klebsiella oxytoca	99.9856	1910	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	conclusive
GCF_002925905.1	s__Klebsiella michiganensis	92.5093	1650	1952	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	91.7114	1622	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_009707385.1	s__Klebsiella oxytoca_C	89.8638	1566	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902158555.1	s__Klebsiella spallanzanii	88.8017	1555	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_003261575.2	s__Klebsiella huaxiensis	87.818	1580	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCF_002042885.1	s__Citrobacter portucalensis	81.3382	820	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_005843885.1	s__Escherichia sp005843885	80.9772	768	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCA_901456055.1	s__Phytobacter ursingii	80.5805	838	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCF_900111105.1	s__Rosenbergiella nectarea	78.5755	112	1952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:33,304] [INFO] GTDB search result was written to GCF_900636985.1_45889_C01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:33,306] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:33,309] [INFO] DFAST_QC result json was written to GCF_900636985.1_45889_C01_genomic.fna/dqc_result.json
[2024-01-25 17:45:33,309] [INFO] DFAST_QC completed!
[2024-01-25 17:45:33,309] [INFO] Total running time: 0h1m28s