[2024-01-24 14:39:01,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,313] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference
[2024-01-24 14:39:02,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:02,596] [INFO] Task started: Prodigal
[2024-01-24 14:39:02,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fadf58d-a6a2-40ce-a0b4-e6ce28e96494/GCF_007970185.1_ASM797018v1_genomic.fna.gz | prodigal -d GCF_007970185.1_ASM797018v1_genomic.fna/cds.fna -a GCF_007970185.1_ASM797018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:48,838] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:48,838] [INFO] Task started: HMMsearch
[2024-01-24 14:39:48,838] [INFO] Running command: hmmsearch --tblout GCF_007970185.1_ASM797018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/reference_markers.hmm GCF_007970185.1_ASM797018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:49,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:49,236] [INFO] Found 6/6 markers.
[2024-01-24 14:39:49,302] [INFO] Query marker FASTA was written to GCF_007970185.1_ASM797018v1_genomic.fna/markers.fasta
[2024-01-24 14:39:49,302] [INFO] Task started: Blastn
[2024-01-24 14:39:49,302] [INFO] Running command: blastn -query GCF_007970185.1_ASM797018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/reference_markers.fasta -out GCF_007970185.1_ASM797018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:49,962] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:49,966] [INFO] Selected 12 target genomes.
[2024-01-24 14:39:49,967] [INFO] Target genome list was writen to GCF_007970185.1_ASM797018v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:49,973] [INFO] Task started: fastANI
[2024-01-24 14:39:49,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fadf58d-a6a2-40ce-a0b4-e6ce28e96494/GCF_007970185.1_ASM797018v1_genomic.fna.gz --refList GCF_007970185.1_ASM797018v1_genomic.fna/target_genomes.txt --output GCF_007970185.1_ASM797018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:06,274] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:06,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:06,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:06,284] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:06,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:06,285] [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
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	100.0	2599	2599	95	conclusive
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	99.9947	2584	2599	95	conclusive
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	77.094	367	2599	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.9897	316	2599	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.7837	253	2599	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.6991	245	2599	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.6819	249	2599	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.6229	213	2599	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.5105	248	2599	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.4231	251	2599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:06,286] [INFO] DFAST Taxonomy check result was written to GCF_007970185.1_ASM797018v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:06,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:06,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:06,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/checkm_data
[2024-01-24 14:40:06,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:06,359] [INFO] Task started: CheckM
[2024-01-24 14:40:06,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007970185.1_ASM797018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007970185.1_ASM797018v1_genomic.fna/checkm_input GCF_007970185.1_ASM797018v1_genomic.fna/checkm_result
[2024-01-24 14:42:03,675] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:03,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:03,701] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:03,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:03,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007970185.1_ASM797018v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:03,702] [INFO] Task started: Blastn
[2024-01-24 14:42:03,702] [INFO] Running command: blastn -query GCF_007970185.1_ASM797018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f43bf7-e95f-4a1c-ae79-fe3b93045d3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007970185.1_ASM797018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:04,512] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:04,518] [INFO] Selected 11 target genomes.
[2024-01-24 14:42:04,518] [INFO] Target genome list was writen to GCF_007970185.1_ASM797018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:04,533] [INFO] Task started: fastANI
[2024-01-24 14:42:04,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fadf58d-a6a2-40ce-a0b4-e6ce28e96494/GCF_007970185.1_ASM797018v1_genomic.fna.gz --refList GCF_007970185.1_ASM797018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007970185.1_ASM797018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:23,535] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:23,546] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:23,547] [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_007970185.1	s__Pseudobacter ginsenosidimutans	100.0	2599	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003991355.1	s__Pseudobacter rhizosphaerae	89.1246	1863	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744805.1	s__Pseudobacter sp017744805	82.7191	1122	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927185.1	s__Pseudobacter sp012927185	80.0108	984	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	77.7798	531	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	77.1327	369	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	77.0642	236	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_011759375.1	s__Paraflavitalea devenefica	76.9808	317	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	76.6837	267	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	76.4231	251	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001898405.1	s__46-32 sp001898405	76.3508	160	2599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:23,550] [INFO] GTDB search result was written to GCF_007970185.1_ASM797018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:23,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:23,555] [INFO] DFAST_QC result json was written to GCF_007970185.1_ASM797018v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:23,556] [INFO] DFAST_QC completed!
[2024-01-24 14:42:23,556] [INFO] Total running time: 0h3m22s