[2024-01-24 14:12:35,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference
[2024-01-24 14:12:37,170] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:37,171] [INFO] Task started: Prodigal
[2024-01-24 14:12:37,171] [INFO] Running command: gunzip -c /var/lib/cwl/stg071c9e08-f0b3-45a2-8523-903ab5f98194/GCF_004342025.1_ASM434202v1_genomic.fna.gz | prodigal -d GCF_004342025.1_ASM434202v1_genomic.fna/cds.fna -a GCF_004342025.1_ASM434202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:03,700] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:03,700] [INFO] Task started: HMMsearch
[2024-01-24 14:13:03,700] [INFO] Running command: hmmsearch --tblout GCF_004342025.1_ASM434202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/reference_markers.hmm GCF_004342025.1_ASM434202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:04,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:04,087] [INFO] Found 6/6 markers.
[2024-01-24 14:13:04,157] [INFO] Query marker FASTA was written to GCF_004342025.1_ASM434202v1_genomic.fna/markers.fasta
[2024-01-24 14:13:04,158] [INFO] Task started: Blastn
[2024-01-24 14:13:04,158] [INFO] Running command: blastn -query GCF_004342025.1_ASM434202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/reference_markers.fasta -out GCF_004342025.1_ASM434202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:05,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:05,358] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:05,358] [INFO] Target genome list was writen to GCF_004342025.1_ASM434202v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:05,368] [INFO] Task started: fastANI
[2024-01-24 14:13:05,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg071c9e08-f0b3-45a2-8523-903ab5f98194/GCF_004342025.1_ASM434202v1_genomic.fna.gz --refList GCF_004342025.1_ASM434202v1_genomic.fna/target_genomes.txt --output GCF_004342025.1_ASM434202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:34,601] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:34,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:34,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:34,619] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:34,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:34,619] [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 turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	88.0723	1861	3029	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	85.7696	2122	3029	95	below_threshold
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	85.7526	2149	3029	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	84.3126	1937	3029	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	84.2932	2015	3029	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	84.2131	1982	3029	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	84.157	1949	3029	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	83.788	1794	3029	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	83.3539	1631	3029	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	83.2513	1758	3029	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	83.1676	1612	3029	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	83.1096	1752	3029	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	83.1095	1632	3029	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	82.6339	1589	3029	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.7807	521	3029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:34,621] [INFO] DFAST Taxonomy check result was written to GCF_004342025.1_ASM434202v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:34,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:34,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:34,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/checkm_data
[2024-01-24 14:13:34,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:34,708] [INFO] Task started: CheckM
[2024-01-24 14:13:34,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342025.1_ASM434202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342025.1_ASM434202v1_genomic.fna/checkm_input GCF_004342025.1_ASM434202v1_genomic.fna/checkm_result
[2024-01-24 14:14:56,697] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:56,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:56,730] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:56,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:56,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342025.1_ASM434202v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:56,732] [INFO] Task started: Blastn
[2024-01-24 14:14:56,732] [INFO] Running command: blastn -query GCF_004342025.1_ASM434202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0766cfe8-8993-4ac6-be71-726d0ad36696/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342025.1_ASM434202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:58,604] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:58,608] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:58,608] [INFO] Target genome list was writen to GCF_004342025.1_ASM434202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:58,662] [INFO] Task started: fastANI
[2024-01-24 14:14:58,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg071c9e08-f0b3-45a2-8523-903ab5f98194/GCF_004342025.1_ASM434202v1_genomic.fna.gz --refList GCF_004342025.1_ASM434202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342025.1_ASM434202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:28,977] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:28,989] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:28,989] [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_004342025.1	s__Kribbella sp004342025	100.0	3026	3029	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_004348725.1	s__Kribbella sp004348725	88.0859	1859	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345665.1	s__Kribbella sp004345665	86.4364	2020	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331485.1	s__Kribbella sp004331485	85.779	2119	3029	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	85.7567	2147	3029	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	84.2789	1981	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_004365875.1	s__Kribbella sp004365875	84.2356	1922	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331435.1	s__Kribbella sindirgiensis	84.2159	1982	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	-
GCF_004217145.1	s__Kribbella soli_A	83.9911	1962	3029	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	83.8026	1791	3029	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	83.3626	1629	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828865.1	s__Kribbella amoyensis	83.2703	1754	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205135.1	s__Kribbella italica	83.1034	1754	3029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548305.1	s__Kribbella sp010548305	82.814	1621	3029	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 14:15:28,990] [INFO] GTDB search result was written to GCF_004342025.1_ASM434202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:28,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:28,996] [INFO] DFAST_QC result json was written to GCF_004342025.1_ASM434202v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:28,997] [INFO] DFAST_QC completed!
[2024-01-24 14:15:28,997] [INFO] Total running time: 0h2m53s