[2024-01-24 13:52:12,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference
[2024-01-24 13:52:13,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,637] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg77b65c98-fc1a-4eb8-8288-9eb8d6dca43b/GCF_006711645.1_ASM671164v1_genomic.fna.gz | prodigal -d GCF_006711645.1_ASM671164v1_genomic.fna/cds.fna -a GCF_006711645.1_ASM671164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:28,815] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:28,815] [INFO] Task started: HMMsearch
[2024-01-24 13:52:28,815] [INFO] Running command: hmmsearch --tblout GCF_006711645.1_ASM671164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/reference_markers.hmm GCF_006711645.1_ASM671164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:29,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:29,142] [INFO] Found 6/6 markers.
[2024-01-24 13:52:29,192] [INFO] Query marker FASTA was written to GCF_006711645.1_ASM671164v1_genomic.fna/markers.fasta
[2024-01-24 13:52:29,192] [INFO] Task started: Blastn
[2024-01-24 13:52:29,192] [INFO] Running command: blastn -query GCF_006711645.1_ASM671164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/reference_markers.fasta -out GCF_006711645.1_ASM671164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:30,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:30,055] [INFO] Selected 22 target genomes.
[2024-01-24 13:52:30,055] [INFO] Target genome list was writen to GCF_006711645.1_ASM671164v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:30,074] [INFO] Task started: fastANI
[2024-01-24 13:52:30,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b65c98-fc1a-4eb8-8288-9eb8d6dca43b/GCF_006711645.1_ASM671164v1_genomic.fna.gz --refList GCF_006711645.1_ASM671164v1_genomic.fna/target_genomes.txt --output GCF_006711645.1_ASM671164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:55,636] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:55,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:55,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:55,658] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:55,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:55,659] [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
Raoultella electrica	strain=DSM 102253	GCA_006711645.1	1259973	1259973	type	True	100.0	1924	1925	95	conclusive
Raoultella ornithinolytica	strain=NBRC 105727	GCA_001598295.1	54291	54291	type	True	93.8458	1444	1925	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	93.5136	1455	1925	95	below_threshold
Raoultella terrigena	strain=NBRC 14941	GCA_006539725.1	577	577	type	True	85.9862	1305	1925	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	85.0822	1332	1925	95	below_threshold
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	84.8866	1316	1925	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	84.506	1272	1925	95	below_threshold
Klebsiella huaxiensis	strain=WCHKl090001	GCA_003261575.2	2153354	2153354	type	True	84.3344	1220	1925	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	84.3247	1200	1925	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	84.2493	1197	1925	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	83.9574	1208	1925	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	83.9385	1204	1925	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.8243	899	1925	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.5466	864	1925	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5023	899	1925	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	81.4051	804	1925	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.3038	901	1925	95	below_threshold
Kosakonia oryzae	strain=Ola 51	GCA_001658025.2	497725	497725	type	True	80.9394	902	1925	95	below_threshold
Kosakonia oryzae	strain=CGMCC 1.7012	GCA_900112145.1	497725	497725	type	True	80.8081	880	1925	95	below_threshold
Kosakonia arachidis	strain=Ah-143	GCA_900116535.1	551989	551989	type	True	80.2042	818	1925	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	79.1237	569	1925	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	78.5513	520	1925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:55,660] [INFO] DFAST Taxonomy check result was written to GCF_006711645.1_ASM671164v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:55,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:55,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:55,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/checkm_data
[2024-01-24 13:52:55,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:55,725] [INFO] Task started: CheckM
[2024-01-24 13:52:55,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006711645.1_ASM671164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006711645.1_ASM671164v1_genomic.fna/checkm_input GCF_006711645.1_ASM671164v1_genomic.fna/checkm_result
[2024-01-24 13:53:42,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:42,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:42,401] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:42,402] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:42,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006711645.1_ASM671164v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:42,403] [INFO] Task started: Blastn
[2024-01-24 13:53:42,403] [INFO] Running command: blastn -query GCF_006711645.1_ASM671164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11eebcb1-9df3-47dc-a3b2-a1ce83c71cf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006711645.1_ASM671164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:43,592] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:43,597] [INFO] Selected 11 target genomes.
[2024-01-24 13:53:43,597] [INFO] Target genome list was writen to GCF_006711645.1_ASM671164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:43,609] [INFO] Task started: fastANI
[2024-01-24 13:53:43,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b65c98-fc1a-4eb8-8288-9eb8d6dca43b/GCF_006711645.1_ASM671164v1_genomic.fna.gz --refList GCF_006711645.1_ASM671164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006711645.1_ASM671164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:56,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:56,820] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:53:56,821] [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_006711645.1	s__Klebsiella electrica	100.0	1924	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.88	98.54	0.89	0.85	7	inconclusive
GCA_009929615.1	s__Frisingicoccus sp009929615	97.0996	62	1925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	inconclusive
GCF_001598295.1	s__Klebsiella ornithinolytica	93.8405	1446	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.42	99.16	0.93	0.81	95	-
GCF_000735435.1	s__Klebsiella planticola	93.5136	1455	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCA_900759445.1	s__Klebsiella sp900759445	90.7234	721	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342285.1	s__Klebsiella sp004342285	88.1208	1321	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014298075.1	s__Klebsiella sp003752615	87.4242	1306	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.02	98.38	0.93	0.91	5	-
GCF_002270295.1	s__Klebsiella sp002270295	86.2669	1358	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	83.0665	1008	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.5533	902	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000280495.2	s__Kosakonia radicincitans	82.1573	973	1925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:56,822] [INFO] GTDB search result was written to GCF_006711645.1_ASM671164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:56,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:56,827] [INFO] DFAST_QC result json was written to GCF_006711645.1_ASM671164v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:56,828] [INFO] DFAST_QC completed!
[2024-01-24 13:53:56,828] [INFO] Total running time: 0h1m44s