[2024-01-24 14:38:46,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:46,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:46,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference
[2024-01-24 14:38:48,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,479] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg5689e95f-ef85-46e0-a9a9-29669a245593/GCF_900706815.1_28745_G01_genomic.fna.gz | prodigal -d GCF_900706815.1_28745_G01_genomic.fna/cds.fna -a GCF_900706815.1_28745_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:55,222] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:55,222] [INFO] Task started: HMMsearch
[2024-01-24 14:38:55,223] [INFO] Running command: hmmsearch --tblout GCF_900706815.1_28745_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/reference_markers.hmm GCF_900706815.1_28745_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:55,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:55,493] [INFO] Found 6/6 markers.
[2024-01-24 14:38:55,525] [INFO] Query marker FASTA was written to GCF_900706815.1_28745_G01_genomic.fna/markers.fasta
[2024-01-24 14:38:55,525] [INFO] Task started: Blastn
[2024-01-24 14:38:55,526] [INFO] Running command: blastn -query GCF_900706815.1_28745_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/reference_markers.fasta -out GCF_900706815.1_28745_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:56,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:56,323] [INFO] Selected 19 target genomes.
[2024-01-24 14:38:56,323] [INFO] Target genome list was writen to GCF_900706815.1_28745_G01_genomic.fna/target_genomes.txt
[2024-01-24 14:38:56,338] [INFO] Task started: fastANI
[2024-01-24 14:38:56,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg5689e95f-ef85-46e0-a9a9-29669a245593/GCF_900706815.1_28745_G01_genomic.fna.gz --refList GCF_900706815.1_28745_G01_genomic.fna/target_genomes.txt --output GCF_900706815.1_28745_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:11,903] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:11,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:11,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:11,919] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:11,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:11,919] [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
Moellerella wisconsensis	strain=NCTC12132	GCA_900706815.1	158849	158849	type	True	100.0	1113	1113	95	conclusive
Moellerella wisconsensis	strain=ATCC 35017	GCA_001294465.1	158849	158849	type	True	99.9476	1076	1113	95	conclusive
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	79.5849	362	1113	95	below_threshold
Providencia rettgeri	strain=FDAARGOS 1450	GCA_019048105.1	587	587	suspected-type	True	79.4939	364	1113	95	below_threshold
Providencia huaxiensis	strain=WCHPr000369	GCA_002843235.3	2027290	2027290	type	True	79.3813	367	1113	95	below_threshold
Providencia heimbachae	strain=NCTC12003	GCA_900475855.1	333962	333962	type	True	79.2438	372	1113	95	below_threshold
Providencia rustigianii	strain=DSM 4541	GCA_000156395.1	158850	158850	type	True	79.2404	337	1113	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.2209	74	1113	95	below_threshold
Providencia burhodogranariea	strain=DSM 19968	GCA_000314855.2	516074	516074	type	True	79.0633	385	1113	95	below_threshold
Providencia vermicola	strain=DSM 17385	GCA_020381325.1	333965	333965	suspected-type	True	78.9087	351	1113	95	below_threshold
Providencia alcalifaciens	strain=DSM 30120	GCA_000173415.1	126385	126385	type	True	78.8955	345	1113	95	below_threshold
Providencia sneebia	strain=DSM 19967	GCA_000314895.2	516075	516075	type	True	78.8952	328	1113	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	78.8818	132	1113	95	below_threshold
Providencia heimbachae	strain=ATCC 35613	GCA_001655055.1	333962	333962	type	True	78.8321	360	1113	95	below_threshold
Providencia thailandensis	strain=KCTC 23281	GCA_014652175.1	990144	990144	type	True	78.6426	374	1113	95	below_threshold
Photorhabdus heterorhabditis	strain=SF41	GCA_018448905.1	880156	880156	type	True	78.2817	178	1113	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.0606	95	1113	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.9856	81	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:11,921] [INFO] DFAST Taxonomy check result was written to GCF_900706815.1_28745_G01_genomic.fna/tc_result.tsv
[2024-01-24 14:39:11,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:11,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:11,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/checkm_data
[2024-01-24 14:39:11,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:11,959] [INFO] Task started: CheckM
[2024-01-24 14:39:11,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900706815.1_28745_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900706815.1_28745_G01_genomic.fna/checkm_input GCF_900706815.1_28745_G01_genomic.fna/checkm_result
[2024-01-24 14:39:38,450] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:38,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:38,481] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:38,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:38,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900706815.1_28745_G01_genomic.fna/markers.fasta)
[2024-01-24 14:39:38,482] [INFO] Task started: Blastn
[2024-01-24 14:39:38,482] [INFO] Running command: blastn -query GCF_900706815.1_28745_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg141e4463-fa2a-4248-8731-27ea81514d42/dqc_reference/reference_markers_gtdb.fasta -out GCF_900706815.1_28745_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:39,516] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:39,521] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:39,521] [INFO] Target genome list was writen to GCF_900706815.1_28745_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:39,563] [INFO] Task started: fastANI
[2024-01-24 14:39:39,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg5689e95f-ef85-46e0-a9a9-29669a245593/GCF_900706815.1_28745_G01_genomic.fna.gz --refList GCF_900706815.1_28745_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900706815.1_28745_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:56,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:56,918] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:56,919] [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_001294465.1	s__Moellerella wisconsensis	99.9476	1076	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Moellerella	95.0	98.96	96.91	0.97	0.90	4	conclusive
GCA_016618195.1	s__Providencia stuartii_A	79.5884	362	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.56	98.52	0.92	0.91	4	-
GCF_013255915.1	s__Providencia rettgeri_D	79.5874	352	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.61	97.24	0.90	0.84	55	-
GCF_010748935.1	s__Providencia vermicola_A	79.5757	372	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.27	99.19	0.95	0.94	4	-
GCA_900455085.1	s__Providencia rettgeri	79.4671	371	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.33	96.16	0.90	0.86	26	-
GCF_013702265.1	s__Providencia rettgeri_F	79.4221	326	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	97.64	96.33	0.91	0.89	3	-
GCF_002843235.3	s__Providencia huaxiensis	79.3625	367	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	98.91	98.69	0.89	0.86	11	-
GCA_900455155.1	s__Providencia stuartii	79.2625	378	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.18	99.04	0.93	0.88	53	-
GCF_003936755.2	s__Providencia rettgeri_E	79.2093	356	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314855.2	s__Providencia burhodogranariea	79.0643	384	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874625.1	s__Providencia rettgeri_A	78.9851	389	1113	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	78.9549	362	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000173415.1	s__Providencia alcalifaciens	78.9019	344	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.05	98.75	0.92	0.89	24	-
GCF_000314895.2	s__Providencia sneebia	78.8757	329	1113	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	78.8477	376	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.80	99.80	0.94	0.94	2	-
GCF_001655055.1	s__Providencia heimbachae	78.8374	359	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia	95.0	99.30	99.03	0.95	0.93	6	-
GCF_001640365.1	s__Arsenophonus triatominarum	78.3611	89	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902713415.1	s__Arsenophonus sp902713415	78.3289	90	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Arsenophonus	95.0	95.88	95.88	0.82	0.82	2	-
GCF_018448905.1	s__Photorhabdus heterorhabditis	78.2632	180	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	98.62	97.27	0.91	0.86	4	-
GCF_003144405.1	s__Proteus cibi	78.0352	240	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.44	99.18	0.92	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:56,923] [INFO] GTDB search result was written to GCF_900706815.1_28745_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:56,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:56,943] [INFO] DFAST_QC result json was written to GCF_900706815.1_28745_G01_genomic.fna/dqc_result.json
[2024-01-24 14:39:56,944] [INFO] DFAST_QC completed!
[2024-01-24 14:39:56,944] [INFO] Total running time: 0h1m10s