[2024-01-24 13:57:41,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference
[2024-01-24 13:57:42,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:42,684] [INFO] Task started: Prodigal
[2024-01-24 13:57:42,684] [INFO] Running command: gunzip -c /var/lib/cwl/stga7980216-3f83-4125-9547-7714c06fd2c3/GCF_020526085.1_ASM2052608v1_genomic.fna.gz | prodigal -d GCF_020526085.1_ASM2052608v1_genomic.fna/cds.fna -a GCF_020526085.1_ASM2052608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:57,391] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:57,392] [INFO] Task started: HMMsearch
[2024-01-24 13:57:57,392] [INFO] Running command: hmmsearch --tblout GCF_020526085.1_ASM2052608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/reference_markers.hmm GCF_020526085.1_ASM2052608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,713] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,764] [INFO] Query marker FASTA was written to GCF_020526085.1_ASM2052608v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,764] [INFO] Task started: Blastn
[2024-01-24 13:57:57,764] [INFO] Running command: blastn -query GCF_020526085.1_ASM2052608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/reference_markers.fasta -out GCF_020526085.1_ASM2052608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,775] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,778] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:58,779] [INFO] Target genome list was writen to GCF_020526085.1_ASM2052608v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,785] [INFO] Task started: fastANI
[2024-01-24 13:57:58,785] [INFO] Running command: fastANI --query /var/lib/cwl/stga7980216-3f83-4125-9547-7714c06fd2c3/GCF_020526085.1_ASM2052608v1_genomic.fna.gz --refList GCF_020526085.1_ASM2052608v1_genomic.fna/target_genomes.txt --output GCF_020526085.1_ASM2052608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:17,931] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:17,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:17,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:17,946] [INFO] Found 15 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:58:17,947] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:17,947] [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 africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	100.0	1811	1813	95	inconclusive
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	99.9766	1692	1813	95	inconclusive
Klebsiella quasivariicola	strain=KPN1705	GCA_002269255.1	2026240	2026240	type	True	95.3408	1582	1813	95	inconclusive
Klebsiella pneumoniae	strain=FDAARGOS_775	GCA_006364295.1	573	573	type	True	95.2616	1554	1813	95	inconclusive
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	95.239	1541	1813	95	inconclusive
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	95.2292	1556	1813	95	inconclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	95.2131	1545	1813	95	inconclusive
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	95.1963	1493	1813	95	inconclusive
Klebsiella pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	95.022	1502	1813	95	inconclusive
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	94.362	1564	1813	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	93.2261	1538	1813	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.9207	903	1813	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.896	903	1813	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.5321	922	1813	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.4159	909	1813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,951] [INFO] DFAST Taxonomy check result was written to GCF_020526085.1_ASM2052608v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:17,952] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:17,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:17,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/checkm_data
[2024-01-24 13:58:17,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:18,011] [INFO] Task started: CheckM
[2024-01-24 13:58:18,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020526085.1_ASM2052608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020526085.1_ASM2052608v1_genomic.fna/checkm_input GCF_020526085.1_ASM2052608v1_genomic.fna/checkm_result
[2024-01-24 13:59:03,953] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:03,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:03,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:03,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020526085.1_ASM2052608v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:03,982] [INFO] Task started: Blastn
[2024-01-24 13:59:03,983] [INFO] Running command: blastn -query GCF_020526085.1_ASM2052608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2c669a-2b7f-4f26-8fa1-ca459c2b49b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_020526085.1_ASM2052608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:05,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:05,437] [INFO] Selected 6 target genomes.
[2024-01-24 13:59:05,437] [INFO] Target genome list was writen to GCF_020526085.1_ASM2052608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:05,438] [INFO] Task started: fastANI
[2024-01-24 13:59:05,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga7980216-3f83-4125-9547-7714c06fd2c3/GCF_020526085.1_ASM2052608v1_genomic.fna.gz --refList GCF_020526085.1_ASM2052608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020526085.1_ASM2052608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:13,553] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,564] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:59:13,564] [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_900978845.1	s__Klebsiella africana	99.9766	1692	1813	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	inconclusive
GCF_000742135.1	s__Klebsiella pneumoniae	95.239	1541	1813	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	inconclusive
GCF_000828055.2	s__Klebsiella variicola	94.362	1564	1813	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	93.1499	1515	1813	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	86.0732	1224	1813	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	82.1422	951	1813	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,566] [INFO] GTDB search result was written to GCF_020526085.1_ASM2052608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:13,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:13,570] [INFO] DFAST_QC result json was written to GCF_020526085.1_ASM2052608v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:13,570] [INFO] DFAST_QC completed!
[2024-01-24 13:59:13,570] [INFO] Total running time: 0h1m32s