[2024-01-24 13:18:42,875] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:42,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:42,878] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference
[2024-01-24 13:18:44,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:44,097] [INFO] Task started: Prodigal
[2024-01-24 13:18:44,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg07b78fa9-f334-407a-8df1-0d2ad06b8e65/GCF_020115515.1_ASM2011551v1_genomic.fna.gz | prodigal -d GCF_020115515.1_ASM2011551v1_genomic.fna/cds.fna -a GCF_020115515.1_ASM2011551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:58,940] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:58,941] [INFO] Task started: HMMsearch
[2024-01-24 13:18:58,941] [INFO] Running command: hmmsearch --tblout GCF_020115515.1_ASM2011551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/reference_markers.hmm GCF_020115515.1_ASM2011551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:59,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:59,260] [INFO] Found 6/6 markers.
[2024-01-24 13:18:59,323] [INFO] Query marker FASTA was written to GCF_020115515.1_ASM2011551v1_genomic.fna/markers.fasta
[2024-01-24 13:18:59,323] [INFO] Task started: Blastn
[2024-01-24 13:18:59,324] [INFO] Running command: blastn -query GCF_020115515.1_ASM2011551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/reference_markers.fasta -out GCF_020115515.1_ASM2011551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,268] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,271] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:00,271] [INFO] Target genome list was writen to GCF_020115515.1_ASM2011551v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:00,277] [INFO] Task started: fastANI
[2024-01-24 13:19:00,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b78fa9-f334-407a-8df1-0d2ad06b8e65/GCF_020115515.1_ASM2011551v1_genomic.fna.gz --refList GCF_020115515.1_ASM2011551v1_genomic.fna/target_genomes.txt --output GCF_020115515.1_ASM2011551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:14,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:14,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:14,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:14,736] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:19:14,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:14,737] [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=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	100.0	1785	1787	95	conclusive
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	99.9998	1784	1787	95	conclusive
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	99.9993	1785	1787	95	conclusive
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	99.989	1764	1787	95	conclusive
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	96.6171	1563	1787	95	conclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	93.831	1548	1787	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	93.7299	1526	1787	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.4339	930	1787	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.0752	917	1787	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.8294	915	1787	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	81.1743	829	1787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,738] [INFO] DFAST Taxonomy check result was written to GCF_020115515.1_ASM2011551v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:14,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:14,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:14,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/checkm_data
[2024-01-24 13:19:14,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:14,792] [INFO] Task started: CheckM
[2024-01-24 13:19:14,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020115515.1_ASM2011551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020115515.1_ASM2011551v1_genomic.fna/checkm_input GCF_020115515.1_ASM2011551v1_genomic.fna/checkm_result
[2024-01-24 13:19:58,254] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:58,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,274] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:58,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:58,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020115515.1_ASM2011551v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:58,275] [INFO] Task started: Blastn
[2024-01-24 13:19:58,275] [INFO] Running command: blastn -query GCF_020115515.1_ASM2011551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc18c10c-5c4b-4af3-8fe4-18925d2f6e16/dqc_reference/reference_markers_gtdb.fasta -out GCF_020115515.1_ASM2011551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:59,783] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:59,786] [INFO] Selected 7 target genomes.
[2024-01-24 13:19:59,787] [INFO] Target genome list was writen to GCF_020115515.1_ASM2011551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:59,798] [INFO] Task started: fastANI
[2024-01-24 13:19:59,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b78fa9-f334-407a-8df1-0d2ad06b8e65/GCF_020115515.1_ASM2011551v1_genomic.fna.gz --refList GCF_020115515.1_ASM2011551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020115515.1_ASM2011551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:08,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:08,817] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:08,817] [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	99.989	1764	1787	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	93.7561	1523	1787	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	93.6182	1586	1787	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	93.1524	1501	1787	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	85.7764	1211	1787	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	82.1525	948	1787	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	81.8189	917	1787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:08,819] [INFO] GTDB search result was written to GCF_020115515.1_ASM2011551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:08,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:08,823] [INFO] DFAST_QC result json was written to GCF_020115515.1_ASM2011551v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:08,823] [INFO] DFAST_QC completed!
[2024-01-24 13:20:08,823] [INFO] Total running time: 0h1m26s