[2024-01-24 11:12:27,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference
[2024-01-24 11:12:29,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,049] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,049] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5150d26-e9be-4666-88eb-6e0e1f30c35c/GCF_003012795.1_ASM301279v1_genomic.fna.gz | prodigal -d GCF_003012795.1_ASM301279v1_genomic.fna/cds.fna -a GCF_003012795.1_ASM301279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:40,297] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:40,298] [INFO] Task started: HMMsearch
[2024-01-24 11:12:40,298] [INFO] Running command: hmmsearch --tblout GCF_003012795.1_ASM301279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/reference_markers.hmm GCF_003012795.1_ASM301279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:40,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:40,620] [INFO] Found 6/6 markers.
[2024-01-24 11:12:40,649] [INFO] Query marker FASTA was written to GCF_003012795.1_ASM301279v1_genomic.fna/markers.fasta
[2024-01-24 11:12:40,650] [INFO] Task started: Blastn
[2024-01-24 11:12:40,650] [INFO] Running command: blastn -query GCF_003012795.1_ASM301279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/reference_markers.fasta -out GCF_003012795.1_ASM301279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:41,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:41,606] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:41,606] [INFO] Target genome list was writen to GCF_003012795.1_ASM301279v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:41,612] [INFO] Task started: fastANI
[2024-01-24 11:12:41,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5150d26-e9be-4666-88eb-6e0e1f30c35c/GCF_003012795.1_ASM301279v1_genomic.fna.gz --refList GCF_003012795.1_ASM301279v1_genomic.fna/target_genomes.txt --output GCF_003012795.1_ASM301279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:54,589] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:54,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:54,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:54,601] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:54,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:54,602] [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
Zobellella taiwanensis	strain=JCM 13381	GCA_003012795.1	347535	347535	type	True	100.0	1170	1174	95	conclusive
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	89.4055	868	1174	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	87.1996	903	1174	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	83.543	751	1174	95	below_threshold
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	83.3008	780	1174	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	82.4817	747	1174	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	82.3311	716	1174	95	below_threshold
Oceanisphaera arctica	strain=KCTC 23013	GCA_014652055.1	641510	641510	type	True	81.8845	707	1174	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.9983	199	1174	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9455	257	1174	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.7713	198	1174	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.6721	210	1174	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.5736	206	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:54,604] [INFO] DFAST Taxonomy check result was written to GCF_003012795.1_ASM301279v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:54,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:54,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:54,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/checkm_data
[2024-01-24 11:12:54,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:54,646] [INFO] Task started: CheckM
[2024-01-24 11:12:54,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012795.1_ASM301279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012795.1_ASM301279v1_genomic.fna/checkm_input GCF_003012795.1_ASM301279v1_genomic.fna/checkm_result
[2024-01-24 11:13:30,164] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:30,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:30,185] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:30,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:30,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012795.1_ASM301279v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:30,187] [INFO] Task started: Blastn
[2024-01-24 11:13:30,187] [INFO] Running command: blastn -query GCF_003012795.1_ASM301279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ba23887-e5eb-4ff6-9f00-450e424b222a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012795.1_ASM301279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:31,841] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:31,845] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:31,845] [INFO] Target genome list was writen to GCF_003012795.1_ASM301279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:31,866] [INFO] Task started: fastANI
[2024-01-24 11:13:31,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5150d26-e9be-4666-88eb-6e0e1f30c35c/GCF_003012795.1_ASM301279v1_genomic.fna.gz --refList GCF_003012795.1_ASM301279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012795.1_ASM301279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:39,592] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:39,599] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:39,599] [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_003012795.1	s__Zobellella_D taiwanensis	100.0	1170	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002237365.1	s__Zobellella denitrificans	89.4198	867	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	87.735	915	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012775.1	s__Zobellella_C endophytica	87.2111	902	1174	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_000243075.1	s__Oceanimonas sp000243075	84.7558	812	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049725.1	s__Oceanimonas marisflavi	83.5452	751	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870485.1	s__Oceanisphaera psychrotolerans	82.4686	749	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907015.1	s__Oceanisphaera litoralis	82.3019	719	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:39,601] [INFO] GTDB search result was written to GCF_003012795.1_ASM301279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:39,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:39,605] [INFO] DFAST_QC result json was written to GCF_003012795.1_ASM301279v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:39,605] [INFO] DFAST_QC completed!
[2024-01-24 11:13:39,605] [INFO] Total running time: 0h1m12s