[2024-01-25 18:00:51,452] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:51,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:51,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference
[2024-01-25 18:00:52,581] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:52,582] [INFO] Task started: Prodigal
[2024-01-25 18:00:52,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bf889b0-aa2a-4c82-889f-390ff337a7e0/GCF_000314855.2_ASM31485v2_genomic.fna.gz | prodigal -d GCF_000314855.2_ASM31485v2_genomic.fna/cds.fna -a GCF_000314855.2_ASM31485v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:00,961] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:00,961] [INFO] Task started: HMMsearch
[2024-01-25 18:01:00,961] [INFO] Running command: hmmsearch --tblout GCF_000314855.2_ASM31485v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/reference_markers.hmm GCF_000314855.2_ASM31485v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:01,186] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:01,187] [INFO] Found 6/6 markers.
[2024-01-25 18:01:01,221] [INFO] Query marker FASTA was written to GCF_000314855.2_ASM31485v2_genomic.fna/markers.fasta
[2024-01-25 18:01:01,222] [INFO] Task started: Blastn
[2024-01-25 18:01:01,222] [INFO] Running command: blastn -query GCF_000314855.2_ASM31485v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/reference_markers.fasta -out GCF_000314855.2_ASM31485v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:01,942] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:01,944] [INFO] Selected 15 target genomes.
[2024-01-25 18:01:01,945] [INFO] Target genome list was writen to GCF_000314855.2_ASM31485v2_genomic.fna/target_genomes.txt
[2024-01-25 18:01:01,953] [INFO] Task started: fastANI
[2024-01-25 18:01:01,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf889b0-aa2a-4c82-889f-390ff337a7e0/GCF_000314855.2_ASM31485v2_genomic.fna.gz --refList GCF_000314855.2_ASM31485v2_genomic.fna/target_genomes.txt --output GCF_000314855.2_ASM31485v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:16,086] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:16,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:16,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:16,096] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:16,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:16,097] [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 burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	99.9999	1518	1522	95	conclusive
Providencia thailandensis	strain=KCTC 23281	GCA_014652175.1	990144	990144	type	True	81.8131	818	1522	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	81.5114	802	1522	95	below_threshold
Providencia sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	80.9446	630	1522	95	below_threshold
Providencia heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	80.0841	687	1522	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	80.0712	614	1522	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	79.9408	628	1522	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	79.9266	563	1522	95	below_threshold
Providencia rustigianii	strain=NCTC11802	GCA_900455075.1	158850	158850	type	True	79.9243	571	1522	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	79.7555	548	1522	95	below_threshold
Providencia vermicola	strain=DSM 17385	GCA_020381325.1	333965	333965	suspected-type	True	79.7205	646	1522	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	76.8207	50	1522	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	76.4689	65	1522	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	76.4175	63	1522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:16,098] [INFO] DFAST Taxonomy check result was written to GCF_000314855.2_ASM31485v2_genomic.fna/tc_result.tsv
[2024-01-25 18:01:16,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:16,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:16,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/checkm_data
[2024-01-25 18:01:16,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:16,145] [INFO] Task started: CheckM
[2024-01-25 18:01:16,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000314855.2_ASM31485v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000314855.2_ASM31485v2_genomic.fna/checkm_input GCF_000314855.2_ASM31485v2_genomic.fna/checkm_result
[2024-01-25 18:01:44,988] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:44,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:45,011] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:45,011] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:45,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000314855.2_ASM31485v2_genomic.fna/markers.fasta)
[2024-01-25 18:01:45,012] [INFO] Task started: Blastn
[2024-01-25 18:01:45,012] [INFO] Running command: blastn -query GCF_000314855.2_ASM31485v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg83953e60-1441-49c4-8a41-4a51ebe9fef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000314855.2_ASM31485v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:46,189] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:46,192] [INFO] Selected 12 target genomes.
[2024-01-25 18:01:46,193] [INFO] Target genome list was writen to GCF_000314855.2_ASM31485v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:46,209] [INFO] Task started: fastANI
[2024-01-25 18:01:46,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf889b0-aa2a-4c82-889f-390ff337a7e0/GCF_000314855.2_ASM31485v2_genomic.fna.gz --refList GCF_000314855.2_ASM31485v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000314855.2_ASM31485v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:57,365] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:57,374] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:57,374] [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_000314855.2	s__Providencia burhodogranariea	99.9999	1518	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900455155.1	s__Providencia stuartii	81.7794	813	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	99.04	0.93	0.88	53	-
GCF_010748935.1	s__Providencia vermicola_A	81.7256	810	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.27	99.19	0.95	0.94	4	-
GCA_016618195.1	s__Providencia stuartii_A	81.5196	801	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.56	98.52	0.92	0.91	4	-
GCF_000314895.2	s__Providencia sneebia	80.9714	627	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533305.1	s__Providencia sp003533305	80.1337	669	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
GCF_000156395.1	s__Providencia rustigianii	79.9351	562	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.28	98.46	0.94	0.90	9	-
GCF_013255915.1	s__Providencia rettgeri_D	79.9209	637	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCF_003936755.2	s__Providencia rettgeri_E	79.8252	621	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173415.1	s__Providencia alcalifaciens	79.76	547	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.05	98.75	0.92	0.89	24	-
GCF_017151615.1	s__Providencia stuartii_C	79.6553	657	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000527275.1	s__Providencia alcalifaciens_A	79.6432	550	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.68	97.24	0.94	0.89	15	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:57,376] [INFO] GTDB search result was written to GCF_000314855.2_ASM31485v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:57,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:57,380] [INFO] DFAST_QC result json was written to GCF_000314855.2_ASM31485v2_genomic.fna/dqc_result.json
[2024-01-25 18:01:57,380] [INFO] DFAST_QC completed!
[2024-01-25 18:01:57,380] [INFO] Total running time: 0h1m6s