[2024-01-25 18:41:35,456] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:35,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:35,458] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference
[2024-01-25 18:41:36,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:36,654] [INFO] Task started: Prodigal
[2024-01-25 18:41:36,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a4ea86c-0685-4c5c-8b27-bfa83b9f6068/GCF_020099175.1_ASM2009917v1_genomic.fna.gz | prodigal -d GCF_020099175.1_ASM2009917v1_genomic.fna/cds.fna -a GCF_020099175.1_ASM2009917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:49,624] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:49,625] [INFO] Task started: HMMsearch
[2024-01-25 18:41:49,625] [INFO] Running command: hmmsearch --tblout GCF_020099175.1_ASM2009917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/reference_markers.hmm GCF_020099175.1_ASM2009917v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:49,933] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:49,934] [INFO] Found 6/6 markers.
[2024-01-25 18:41:49,995] [INFO] Query marker FASTA was written to GCF_020099175.1_ASM2009917v1_genomic.fna/markers.fasta
[2024-01-25 18:41:49,995] [INFO] Task started: Blastn
[2024-01-25 18:41:49,995] [INFO] Running command: blastn -query GCF_020099175.1_ASM2009917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/reference_markers.fasta -out GCF_020099175.1_ASM2009917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:50,910] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:50,913] [INFO] Selected 11 target genomes.
[2024-01-25 18:41:50,913] [INFO] Target genome list was writen to GCF_020099175.1_ASM2009917v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:50,917] [INFO] Task started: fastANI
[2024-01-25 18:41:50,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4ea86c-0685-4c5c-8b27-bfa83b9f6068/GCF_020099175.1_ASM2009917v1_genomic.fna.gz --refList GCF_020099175.1_ASM2009917v1_genomic.fna/target_genomes.txt --output GCF_020099175.1_ASM2009917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:05,464] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:05,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:05,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:05,472] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:42:05,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:05,473] [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 quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	100.0	1832	1832	95	conclusive
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	99.9999	1830	1832	95	conclusive
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	99.9816	1784	1832	95	conclusive
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	99.9776	1787	1832	95	conclusive
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	96.5815	1615	1832	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	93.8428	1564	1832	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	93.737	1566	1832	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.4359	939	1832	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.0052	945	1832	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.8595	911	1832	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.2678	860	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:05,474] [INFO] DFAST Taxonomy check result was written to GCF_020099175.1_ASM2009917v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:05,474] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:05,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:05,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/checkm_data
[2024-01-25 18:42:05,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:05,538] [INFO] Task started: CheckM
[2024-01-25 18:42:05,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020099175.1_ASM2009917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020099175.1_ASM2009917v1_genomic.fna/checkm_input GCF_020099175.1_ASM2009917v1_genomic.fna/checkm_result
[2024-01-25 18:42:43,909] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:43,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:43,929] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:43,929] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:43,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020099175.1_ASM2009917v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:43,930] [INFO] Task started: Blastn
[2024-01-25 18:42:43,930] [INFO] Running command: blastn -query GCF_020099175.1_ASM2009917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8ef9d3b-998a-43f3-93c4-24df152ac1ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_020099175.1_ASM2009917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:45,388] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:45,392] [INFO] Selected 7 target genomes.
[2024-01-25 18:42:45,392] [INFO] Target genome list was writen to GCF_020099175.1_ASM2009917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:45,398] [INFO] Task started: fastANI
[2024-01-25 18:42:45,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a4ea86c-0685-4c5c-8b27-bfa83b9f6068/GCF_020099175.1_ASM2009917v1_genomic.fna.gz --refList GCF_020099175.1_ASM2009917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020099175.1_ASM2009917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:54,673] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:54,679] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:54,679] [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_000751755.1	s__Klebsiella quasipneumoniae	99.9816	1784	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	conclusive
GCF_000742135.1	s__Klebsiella pneumoniae	93.7421	1557	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_000828055.2	s__Klebsiella variicola	93.7142	1600	1832	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	93.157	1514	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000215745.1	s__Klebsiella aerogenes	85.9157	1251	1832	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	82.4172	970	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_002939185.1	s__Enterobacter sichuanensis	81.8587	916	1832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:54,681] [INFO] GTDB search result was written to GCF_020099175.1_ASM2009917v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:54,681] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:54,685] [INFO] DFAST_QC result json was written to GCF_020099175.1_ASM2009917v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:54,685] [INFO] DFAST_QC completed!
[2024-01-25 18:42:54,685] [INFO] Total running time: 0h1m19s