[2024-01-24 12:13:59,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:59,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:59,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference
[2024-01-24 12:14:00,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,482] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,483] [INFO] Running command: gunzip -c /var/lib/cwl/stga4f9f61a-af48-484f-975e-4bdf389034b0/GCF_002843235.3_ASM284323v3_genomic.fna.gz | prodigal -d GCF_002843235.3_ASM284323v3_genomic.fna/cds.fna -a GCF_002843235.3_ASM284323v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:11,968] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:11,968] [INFO] Task started: HMMsearch
[2024-01-24 12:14:11,968] [INFO] Running command: hmmsearch --tblout GCF_002843235.3_ASM284323v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/reference_markers.hmm GCF_002843235.3_ASM284323v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:12,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:12,330] [INFO] Found 6/6 markers.
[2024-01-24 12:14:12,378] [INFO] Query marker FASTA was written to GCF_002843235.3_ASM284323v3_genomic.fna/markers.fasta
[2024-01-24 12:14:12,378] [INFO] Task started: Blastn
[2024-01-24 12:14:12,378] [INFO] Running command: blastn -query GCF_002843235.3_ASM284323v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/reference_markers.fasta -out GCF_002843235.3_ASM284323v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:13,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:13,232] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:13,232] [INFO] Target genome list was writen to GCF_002843235.3_ASM284323v3_genomic.fna/target_genomes.txt
[2024-01-24 12:14:13,237] [INFO] Task started: fastANI
[2024-01-24 12:14:13,238] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f9f61a-af48-484f-975e-4bdf389034b0/GCF_002843235.3_ASM284323v3_genomic.fna.gz --refList GCF_002843235.3_ASM284323v3_genomic.fna/target_genomes.txt --output GCF_002843235.3_ASM284323v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:26,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:26,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:26,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:26,326] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:26,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:26,326] [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
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	100.0	1593	1596	95	conclusive
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	91.4633	1230	1596	95	below_threshold
Providencia vermicola	strain=DSM 17385	GCA_020381325.1	333965	333965	suspected-type	True	83.07	1017	1596	95	below_threshold
Providencia heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	81.3768	864	1596	95	below_threshold
Providencia heimbachae	strain=ATCC 35613	GCA_001655055.1	333962	333962	type	True	81.1269	857	1596	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	81.0048	717	1596	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	80.9504	675	1596	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	80.8184	710	1596	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	80.4682	646	1596	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	79.8991	622	1596	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	79.6712	140	1596	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.0365	111	1596	95	below_threshold
Arsenophonus apicola	strain=ArsBeeUS	GCA_020268605.1	2879119	2879119	type	True	78.2973	156	1596	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	77.9376	173	1596	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:26,328] [INFO] DFAST Taxonomy check result was written to GCF_002843235.3_ASM284323v3_genomic.fna/tc_result.tsv
[2024-01-24 12:14:26,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:26,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:26,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/checkm_data
[2024-01-24 12:14:26,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:26,378] [INFO] Task started: CheckM
[2024-01-24 12:14:26,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002843235.3_ASM284323v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002843235.3_ASM284323v3_genomic.fna/checkm_input GCF_002843235.3_ASM284323v3_genomic.fna/checkm_result
[2024-01-24 12:15:04,663] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:04,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,694] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:04,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:04,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002843235.3_ASM284323v3_genomic.fna/markers.fasta)
[2024-01-24 12:15:04,695] [INFO] Task started: Blastn
[2024-01-24 12:15:04,695] [INFO] Running command: blastn -query GCF_002843235.3_ASM284323v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgede68e1b-7c69-4074-8ec4-38b0e5623964/dqc_reference/reference_markers_gtdb.fasta -out GCF_002843235.3_ASM284323v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:05,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:05,829] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:05,829] [INFO] Target genome list was writen to GCF_002843235.3_ASM284323v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:05,834] [INFO] Task started: fastANI
[2024-01-24 12:15:05,834] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f9f61a-af48-484f-975e-4bdf389034b0/GCF_002843235.3_ASM284323v3_genomic.fna.gz --refList GCF_002843235.3_ASM284323v3_genomic.fna/target_genomes_gtdb.txt --output GCF_002843235.3_ASM284323v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:15,147] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,162] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:15,163] [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_002843235.3	s__Providencia huaxiensis	100.0	1593	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.91	98.69	0.89	0.86	11	conclusive
GCF_003936755.2	s__Providencia rettgeri_E	94.1219	1274	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013255915.1	s__Providencia rettgeri_D	92.3335	1296	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCA_900455085.1	s__Providencia rettgeri	91.4128	1244	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.33	96.16	0.90	0.86	26	-
GCF_001874625.1	s__Providencia rettgeri_A	84.6114	1119	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	98.88	0.92	0.87	38	-
GCF_017151615.1	s__Providencia stuartii_C	83.4137	1041	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_001655055.1	s__Providencia heimbachae	81.1191	858	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.30	99.03	0.95	0.93	6	-
GCA_003533305.1	s__Providencia sp003533305	80.7624	826	1596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,166] [INFO] GTDB search result was written to GCF_002843235.3_ASM284323v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:15,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:15,173] [INFO] DFAST_QC result json was written to GCF_002843235.3_ASM284323v3_genomic.fna/dqc_result.json
[2024-01-24 12:15:15,173] [INFO] DFAST_QC completed!
[2024-01-24 12:15:15,173] [INFO] Total running time: 0h1m16s