[2024-01-24 14:55:51,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,288] [INFO] DQC Reference Directory: /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference
[2024-01-24 14:55:52,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,592] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7b16c5f-6338-4f25-b455-da5a7a230752/GCF_002242685.1_ASM224268v1_genomic.fna.gz | prodigal -d GCF_002242685.1_ASM224268v1_genomic.fna/cds.fna -a GCF_002242685.1_ASM224268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:04,798] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:04,798] [INFO] Task started: HMMsearch
[2024-01-24 14:56:04,798] [INFO] Running command: hmmsearch --tblout GCF_002242685.1_ASM224268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/reference_markers.hmm GCF_002242685.1_ASM224268v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:05,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:05,081] [INFO] Found 6/6 markers.
[2024-01-24 14:56:05,113] [INFO] Query marker FASTA was written to GCF_002242685.1_ASM224268v1_genomic.fna/markers.fasta
[2024-01-24 14:56:05,113] [INFO] Task started: Blastn
[2024-01-24 14:56:05,113] [INFO] Running command: blastn -query GCF_002242685.1_ASM224268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/reference_markers.fasta -out GCF_002242685.1_ASM224268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:06,034] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:06,041] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:06,041] [INFO] Target genome list was writen to GCF_002242685.1_ASM224268v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:06,060] [INFO] Task started: fastANI
[2024-01-24 14:56:06,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b16c5f-6338-4f25-b455-da5a7a230752/GCF_002242685.1_ASM224268v1_genomic.fna.gz --refList GCF_002242685.1_ASM224268v1_genomic.fna/target_genomes.txt --output GCF_002242685.1_ASM224268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:15,144] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:15,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:15,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:15,162] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:15,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:15,162] [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
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	100.0	1268	1268	95	conclusive
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	88.5072	882	1268	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	83.9077	799	1268	95	below_threshold
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	83.2662	831	1268	95	below_threshold
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	83.2135	834	1268	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	82.7346	814	1268	95	below_threshold
Oceanisphaera pacifica	strain=DM8	GCA_017498065.1	2818389	2818389	type	True	77.1838	128	1268	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3813	129	1268	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3006	168	1268	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.2799	129	1268	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	75.8928	126	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,164] [INFO] DFAST Taxonomy check result was written to GCF_002242685.1_ASM224268v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:15,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:15,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:15,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/checkm_data
[2024-01-24 14:56:15,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,204] [INFO] Task started: CheckM
[2024-01-24 14:56:15,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002242685.1_ASM224268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002242685.1_ASM224268v1_genomic.fna/checkm_input GCF_002242685.1_ASM224268v1_genomic.fna/checkm_result
[2024-01-24 14:56:53,787] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:53,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:53,830] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:53,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:53,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002242685.1_ASM224268v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:53,832] [INFO] Task started: Blastn
[2024-01-24 14:56:53,833] [INFO] Running command: blastn -query GCF_002242685.1_ASM224268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4a2e843-7c16-45d3-b3ef-29967bbe7a1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002242685.1_ASM224268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:55,550] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:55,553] [INFO] Selected 8 target genomes.
[2024-01-24 14:56:55,554] [INFO] Target genome list was writen to GCF_002242685.1_ASM224268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:55,564] [INFO] Task started: fastANI
[2024-01-24 14:56:55,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b16c5f-6338-4f25-b455-da5a7a230752/GCF_002242685.1_ASM224268v1_genomic.fna.gz --refList GCF_002242685.1_ASM224268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002242685.1_ASM224268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:02,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:02,626] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:02,626] [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_002242685.1	s__Oceanimonas doudoroffii	100.0	1268	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	conclusive
GCF_003049725.1	s__Oceanimonas marisflavi	88.4999	883	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243075.1	s__Oceanimonas sp000243075	86.9865	916	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381965.1	s__Oceanimonas smirnovii	83.9243	798	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012795.1	s__Zobellella_D taiwanensis	83.2339	784	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245495.1	s__Oceanimonas baumannii	83.219	833	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003012775.1	s__Zobellella_C endophytica	82.7174	816	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075035.1	s__Zobellella_A maritima	80.6845	673	1268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:02,629] [INFO] GTDB search result was written to GCF_002242685.1_ASM224268v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:02,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:02,632] [INFO] DFAST_QC result json was written to GCF_002242685.1_ASM224268v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:02,632] [INFO] DFAST_QC completed!
[2024-01-24 14:57:02,632] [INFO] Total running time: 0h1m11s