[2024-01-24 13:40:42,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference
[2024-01-24 13:40:43,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,760] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg426d83c1-4cf7-4984-be92-876802cc6085/GCF_003601925.1_ASM360192v1_genomic.fna.gz | prodigal -d GCF_003601925.1_ASM360192v1_genomic.fna/cds.fna -a GCF_003601925.1_ASM360192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,248] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,248] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,248] [INFO] Running command: hmmsearch --tblout GCF_003601925.1_ASM360192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/reference_markers.hmm GCF_003601925.1_ASM360192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,603] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,648] [INFO] Query marker FASTA was written to GCF_003601925.1_ASM360192v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,649] [INFO] Task started: Blastn
[2024-01-24 13:40:58,649] [INFO] Running command: blastn -query GCF_003601925.1_ASM360192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/reference_markers.fasta -out GCF_003601925.1_ASM360192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,578] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:59,579] [INFO] Target genome list was writen to GCF_003601925.1_ASM360192v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,583] [INFO] Task started: fastANI
[2024-01-24 13:40:59,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg426d83c1-4cf7-4984-be92-876802cc6085/GCF_003601925.1_ASM360192v1_genomic.fna.gz --refList GCF_003601925.1_ASM360192v1_genomic.fna/target_genomes.txt --output GCF_003601925.1_ASM360192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,533] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,545] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:14,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,545] [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
Buttiauxella izardii	strain=CCUG 35510	GCA_003601925.1	82991	82991	type	True	100.0	1550	1553	95	conclusive
Buttiauxella agrestis	strain=NCTC12119	GCA_900446255.1	82977	82977	type	True	89.3381	1330	1553	95	below_threshold
Buttiauxella agrestis	strain=ATCC 33320	GCA_000735355.1	82977	82977	type	True	89.2321	1283	1553	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	87.8204	1187	1553	95	below_threshold
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	86.7279	996	1553	95	below_threshold
Buttiauxella brennerae	strain=ATCC 51605	GCA_001654925.1	82988	82988	type	True	86.6039	1208	1553	95	below_threshold
Buttiauxella gaviniae	strain=ATCC 51604	GCA_001654835.1	82990	82990	type	True	86.4988	1187	1553	95	below_threshold
Buttiauxella ferragutiae	strain=ATCC 51602	GCA_001654915.1	82989	82989	type	True	86.3113	1176	1553	95	below_threshold
Buttiauxella noackiae	strain=ATCC 51607	GCA_001654865.1	82992	82992	type	True	86.1466	1153	1553	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.071	699	1553	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.9168	696	1553	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	79.8368	687	1553	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	79.6685	692	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,547] [INFO] DFAST Taxonomy check result was written to GCF_003601925.1_ASM360192v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/checkm_data
[2024-01-24 13:41:14,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,596] [INFO] Task started: CheckM
[2024-01-24 13:41:14,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003601925.1_ASM360192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003601925.1_ASM360192v1_genomic.fna/checkm_input GCF_003601925.1_ASM360192v1_genomic.fna/checkm_result
[2024-01-24 13:41:59,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:59,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,775] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:59,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:59,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003601925.1_ASM360192v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:59,776] [INFO] Task started: Blastn
[2024-01-24 13:41:59,776] [INFO] Running command: blastn -query GCF_003601925.1_ASM360192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc40e77c8-ef14-44dd-bd75-286aa73aea3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003601925.1_ASM360192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,130] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,133] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:01,134] [INFO] Target genome list was writen to GCF_003601925.1_ASM360192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,148] [INFO] Task started: fastANI
[2024-01-24 13:42:01,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg426d83c1-4cf7-4984-be92-876802cc6085/GCF_003601925.1_ASM360192v1_genomic.fna.gz --refList GCF_003601925.1_ASM360192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003601925.1_ASM360192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:13,145] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,157] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:13,157] [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_003601925.1	s__Buttiauxella izardii	100.0	1550	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000735355.1	s__Buttiauxella agrestis	89.2321	1283	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	96.92	96.37	0.91	0.90	3	-
GCF_902500225.1	s__Buttiauxella agrestis_A	87.8204	1187	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	95.69	95.69	0.85	0.85	2	-
GCF_003818135.1	s__Buttiauxella warmboldiae	86.7344	995	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654925.1	s__Buttiauxella brennerae	86.6042	1208	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654835.1	s__Buttiauxella gaviniae	86.4988	1187	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	98.46	98.46	0.87	0.87	2	-
GCF_001654915.1	s__Buttiauxella ferragutiae	86.2845	1180	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.06	98.93	0.93	0.91	3	-
GCF_001654865.1	s__Buttiauxella noackiae	86.1544	1152	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	98.49	98.49	0.92	0.92	2	-
GCF_014189855.1	s__Buttiauxella sp014189855	85.8108	1160	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006376615.1	s__Buttiauxella sp006376615	85.587	1145	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,159] [INFO] GTDB search result was written to GCF_003601925.1_ASM360192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:13,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:13,163] [INFO] DFAST_QC result json was written to GCF_003601925.1_ASM360192v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:13,163] [INFO] DFAST_QC completed!
[2024-01-24 13:42:13,163] [INFO] Total running time: 0h1m31s