[2024-01-24 11:20:34,061] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference
[2024-01-24 11:20:35,281] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,282] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg396f3aba-96e3-45d8-bd4d-55712aa3aab1/GCF_900447225.1_51726_D01_genomic.fna.gz | prodigal -d GCF_900447225.1_51726_D01_genomic.fna/cds.fna -a GCF_900447225.1_51726_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:45,602] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:45,603] [INFO] Task started: HMMsearch
[2024-01-24 11:20:45,603] [INFO] Running command: hmmsearch --tblout GCF_900447225.1_51726_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/reference_markers.hmm GCF_900447225.1_51726_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:45,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:45,869] [INFO] Found 6/6 markers.
[2024-01-24 11:20:45,901] [INFO] Query marker FASTA was written to GCF_900447225.1_51726_D01_genomic.fna/markers.fasta
[2024-01-24 11:20:45,902] [INFO] Task started: Blastn
[2024-01-24 11:20:45,902] [INFO] Running command: blastn -query GCF_900447225.1_51726_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/reference_markers.fasta -out GCF_900447225.1_51726_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:46,724] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:46,728] [INFO] Selected 16 target genomes.
[2024-01-24 11:20:46,729] [INFO] Target genome list was writen to GCF_900447225.1_51726_D01_genomic.fna/target_genomes.txt
[2024-01-24 11:20:46,741] [INFO] Task started: fastANI
[2024-01-24 11:20:46,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg396f3aba-96e3-45d8-bd4d-55712aa3aab1/GCF_900447225.1_51726_D01_genomic.fna.gz --refList GCF_900447225.1_51726_D01_genomic.fna/target_genomes.txt --output GCF_900447225.1_51726_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:01,840] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:01,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:01,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:01,863] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:01,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:01,864] [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
Edwardsiella ictaluri	strain=NCTC12122	GCA_900447225.1	67780	67780	type	True	100.0	1284	1286	95	conclusive
Edwardsiella ictaluri	strain=ATCC 33202	GCA_000264785.1	67780	67780	type	True	99.9128	1176	1286	95	conclusive
Edwardsiella anguillarum	strain=ET080813	GCA_000264765.2	1821960	1821960	type	True	92.8756	1087	1286	95	below_threshold
Edwardsiella anguillarum	strain=CCUG 64215	GCA_008801815.1	1821960	1821960	type	True	92.7607	1081	1286	95	below_threshold
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	92.4982	1041	1286	95	below_threshold
Edwardsiella tarda	strain=ATCC 15947	GCA_003113495.2	636	636	type	True	83.4414	852	1286	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.0883	479	1286	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8942	478	1286	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.7209	458	1286	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.9911	275	1286	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.5482	262	1286	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	76.6998	97	1286	95	below_threshold
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	76.6353	87	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:01,866] [INFO] DFAST Taxonomy check result was written to GCF_900447225.1_51726_D01_genomic.fna/tc_result.tsv
[2024-01-24 11:21:01,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:01,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:01,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/checkm_data
[2024-01-24 11:21:01,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:01,909] [INFO] Task started: CheckM
[2024-01-24 11:21:01,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447225.1_51726_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447225.1_51726_D01_genomic.fna/checkm_input GCF_900447225.1_51726_D01_genomic.fna/checkm_result
[2024-01-24 11:21:35,901] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:35,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:35,924] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:35,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:35,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447225.1_51726_D01_genomic.fna/markers.fasta)
[2024-01-24 11:21:35,925] [INFO] Task started: Blastn
[2024-01-24 11:21:35,925] [INFO] Running command: blastn -query GCF_900447225.1_51726_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg8619538e-c2d5-48ad-96b6-f399d0f153a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447225.1_51726_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:37,040] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:37,044] [INFO] Selected 10 target genomes.
[2024-01-24 11:21:37,044] [INFO] Target genome list was writen to GCF_900447225.1_51726_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:37,054] [INFO] Task started: fastANI
[2024-01-24 11:21:37,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg396f3aba-96e3-45d8-bd4d-55712aa3aab1/GCF_900447225.1_51726_D01_genomic.fna.gz --refList GCF_900447225.1_51726_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447225.1_51726_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:45,964] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:45,977] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:45,977] [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_000264785.1	s__Edwardsiella ictaluri	99.9128	1176	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.74	99.41	0.96	0.93	11	conclusive
GCF_000264765.2	s__Edwardsiella anguillarum	92.8654	1087	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.66	0.99	0.97	9	-
GCF_001896205.1	s__Edwardsiella piscicida	92.4982	1041	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000341505.1	s__Edwardsiella tarda	83.4676	842	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	-
GCF_000474215.1	s__Edwardsiella hoshinae	82.6073	787	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
GCF_000404125.1	s__Erwinia tracheiphila	79.5308	152	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.22	98.89	0.92	0.87	3	-
GCF_003846135.1	s__Erwinia psidii	79.0758	194	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019132875.1	s__Erwinia sp019132875	77.5371	262	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	76.7231	96	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100175.1	s__Ferrimonas sediminum	76.656	85	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:45,979] [INFO] GTDB search result was written to GCF_900447225.1_51726_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:45,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:45,983] [INFO] DFAST_QC result json was written to GCF_900447225.1_51726_D01_genomic.fna/dqc_result.json
[2024-01-24 11:21:45,983] [INFO] DFAST_QC completed!
[2024-01-24 11:21:45,983] [INFO] Total running time: 0h1m12s