[2024-01-25 19:39:20,402] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:20,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:20,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference
[2024-01-25 19:39:21,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:21,549] [INFO] Task started: Prodigal
[2024-01-25 19:39:21,549] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfeab0b8-8b55-4313-bfb3-58ea0f8b931a/GCF_000828055.2_ASM82805v2_genomic.fna.gz | prodigal -d GCF_000828055.2_ASM82805v2_genomic.fna/cds.fna -a GCF_000828055.2_ASM82805v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:34,659] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:34,659] [INFO] Task started: HMMsearch
[2024-01-25 19:39:34,659] [INFO] Running command: hmmsearch --tblout GCF_000828055.2_ASM82805v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/reference_markers.hmm GCF_000828055.2_ASM82805v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:34,951] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:34,952] [INFO] Found 6/6 markers.
[2024-01-25 19:39:35,008] [INFO] Query marker FASTA was written to GCF_000828055.2_ASM82805v2_genomic.fna/markers.fasta
[2024-01-25 19:39:35,009] [INFO] Task started: Blastn
[2024-01-25 19:39:35,009] [INFO] Running command: blastn -query GCF_000828055.2_ASM82805v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/reference_markers.fasta -out GCF_000828055.2_ASM82805v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:35,892] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:35,897] [INFO] Selected 10 target genomes.
[2024-01-25 19:39:35,897] [INFO] Target genome list was writen to GCF_000828055.2_ASM82805v2_genomic.fna/target_genomes.txt
[2024-01-25 19:39:35,900] [INFO] Task started: fastANI
[2024-01-25 19:39:35,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfeab0b8-8b55-4313-bfb3-58ea0f8b931a/GCF_000828055.2_ASM82805v2_genomic.fna.gz --refList GCF_000828055.2_ASM82805v2_genomic.fna/target_genomes.txt --output GCF_000828055.2_ASM82805v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:47,934] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:47,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:47,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:47,943] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:39:47,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:47,943] [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 variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	100.0	1840	1840	95	conclusive
Klebsiella variicola subsp. variicola	strain=F2R9T	GCA_020525545.1	2590157	244366	type	True	99.9949	1839	1840	95	conclusive
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	99.9921	1837	1840	95	conclusive
Klebsiella variicola	strain=DSM 15968	GCA_020115545.1	244366	244366	type	True	99.9801	1795	1840	95	conclusive
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	99.9736	1788	1840	95	conclusive
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	94.7846	1563	1840	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.0133	922	1840	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8405	932	1840	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.7116	915	1840	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.6906	934	1840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:47,945] [INFO] DFAST Taxonomy check result was written to GCF_000828055.2_ASM82805v2_genomic.fna/tc_result.tsv
[2024-01-25 19:39:47,945] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:47,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:47,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/checkm_data
[2024-01-25 19:39:47,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:47,999] [INFO] Task started: CheckM
[2024-01-25 19:39:47,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000828055.2_ASM82805v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000828055.2_ASM82805v2_genomic.fna/checkm_input GCF_000828055.2_ASM82805v2_genomic.fna/checkm_result
[2024-01-25 19:40:27,814] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:27,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:27,833] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:27,833] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:27,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000828055.2_ASM82805v2_genomic.fna/markers.fasta)
[2024-01-25 19:40:27,834] [INFO] Task started: Blastn
[2024-01-25 19:40:27,834] [INFO] Running command: blastn -query GCF_000828055.2_ASM82805v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8431308-f956-4dfb-b5f4-410307ec6e3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000828055.2_ASM82805v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:29,288] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:29,291] [INFO] Selected 6 target genomes.
[2024-01-25 19:40:29,291] [INFO] Target genome list was writen to GCF_000828055.2_ASM82805v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:29,296] [INFO] Task started: fastANI
[2024-01-25 19:40:29,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfeab0b8-8b55-4313-bfb3-58ea0f8b931a/GCF_000828055.2_ASM82805v2_genomic.fna.gz --refList GCF_000828055.2_ASM82805v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000828055.2_ASM82805v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:37,620] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:37,626] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:37,626] [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_000828055.2	s__Klebsiella variicola	100.0	1840	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	conclusive
GCF_000742135.1	s__Klebsiella pneumoniae	94.804	1548	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_900978845.1	s__Klebsiella africana	94.2209	1555	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	93.6392	1583	1840	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	86.4684	1237	1840	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	82.2148	962	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:37,628] [INFO] GTDB search result was written to GCF_000828055.2_ASM82805v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:37,628] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:37,630] [INFO] DFAST_QC result json was written to GCF_000828055.2_ASM82805v2_genomic.fna/dqc_result.json
[2024-01-25 19:40:37,631] [INFO] DFAST_QC completed!
[2024-01-25 19:40:37,631] [INFO] Total running time: 0h1m17s