[2024-01-24 14:30:45,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference
[2024-01-24 14:30:47,238] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:47,239] [INFO] Task started: Prodigal
[2024-01-24 14:30:47,239] [INFO] Running command: gunzip -c /var/lib/cwl/stg89781e3c-ff13-4643-9298-6371a8689954/GCF_004365875.1_ASM436587v1_genomic.fna.gz | prodigal -d GCF_004365875.1_ASM436587v1_genomic.fna/cds.fna -a GCF_004365875.1_ASM436587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:11,198] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:11,199] [INFO] Task started: HMMsearch
[2024-01-24 14:31:11,199] [INFO] Running command: hmmsearch --tblout GCF_004365875.1_ASM436587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/reference_markers.hmm GCF_004365875.1_ASM436587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:11,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:11,721] [INFO] Found 6/6 markers.
[2024-01-24 14:31:11,788] [INFO] Query marker FASTA was written to GCF_004365875.1_ASM436587v1_genomic.fna/markers.fasta
[2024-01-24 14:31:11,789] [INFO] Task started: Blastn
[2024-01-24 14:31:11,789] [INFO] Running command: blastn -query GCF_004365875.1_ASM436587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/reference_markers.fasta -out GCF_004365875.1_ASM436587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,214] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,218] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:13,219] [INFO] Target genome list was writen to GCF_004365875.1_ASM436587v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,224] [INFO] Task started: fastANI
[2024-01-24 14:31:13,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg89781e3c-ff13-4643-9298-6371a8689954/GCF_004365875.1_ASM436587v1_genomic.fna.gz --refList GCF_004365875.1_ASM436587v1_genomic.fna/target_genomes.txt --output GCF_004365875.1_ASM436587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:41,362] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:41,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:41,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:41,374] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:41,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:41,375] [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
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	88.3925	2242	2772	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	87.3018	2128	2772	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	86.8643	2117	2772	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	86.7336	2086	2772	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	86.283	1976	2772	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	86.23	1970	2772	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	85.0979	1801	2772	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	84.6885	1915	2772	95	below_threshold
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	84.6442	1937	2772	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	84.2315	1560	2772	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	83.039	1590	2772	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	82.9199	1605	2772	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.8187	492	2772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:41,377] [INFO] DFAST Taxonomy check result was written to GCF_004365875.1_ASM436587v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:41,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:41,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:41,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/checkm_data
[2024-01-24 14:31:41,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:41,466] [INFO] Task started: CheckM
[2024-01-24 14:31:41,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365875.1_ASM436587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365875.1_ASM436587v1_genomic.fna/checkm_input GCF_004365875.1_ASM436587v1_genomic.fna/checkm_result
[2024-01-24 14:32:52,139] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:52,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:52,168] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:52,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:52,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365875.1_ASM436587v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:52,169] [INFO] Task started: Blastn
[2024-01-24 14:32:52,169] [INFO] Running command: blastn -query GCF_004365875.1_ASM436587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5faaab-6e95-4e13-95f5-4157cef46be1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365875.1_ASM436587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:54,091] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:54,095] [INFO] Selected 13 target genomes.
[2024-01-24 14:32:54,095] [INFO] Target genome list was writen to GCF_004365875.1_ASM436587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:54,105] [INFO] Task started: fastANI
[2024-01-24 14:32:54,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg89781e3c-ff13-4643-9298-6371a8689954/GCF_004365875.1_ASM436587v1_genomic.fna.gz --refList GCF_004365875.1_ASM436587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365875.1_ASM436587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:21,822] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:21,834] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:21,834] [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_004365875.1	s__Kribbella sp004365875	100.0	2772	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005233875.1	s__Kribbella sp005233875	88.4034	2243	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217145.1	s__Kribbella soli_A	88.1484	2225	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365355.1	s__Kribbella sp004365355	87.9353	2165	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331345.1	s__Kribbella soli	87.3013	2128	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216905.1	s__Kribbella sp004216905	87.1458	2109	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	86.9667	2061	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_004331435.1	s__Kribbella sindirgiensis	86.7552	2084	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	-
GCF_011761605.1	s__Kribbella shirazensis	86.3018	1972	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	86.2268	1970	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205295.1	s__Kribbella solani	85.09	1803	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331465.1	s__Kribbella pittospori	84.6245	1943	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342025.1	s__Kribbella sp004342025	84.4112	1900	2772	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:21,836] [INFO] GTDB search result was written to GCF_004365875.1_ASM436587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:21,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:21,840] [INFO] DFAST_QC result json was written to GCF_004365875.1_ASM436587v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:21,840] [INFO] DFAST_QC completed!
[2024-01-24 14:33:21,840] [INFO] Total running time: 0h2m36s