[2024-01-24 12:21:59,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference
[2024-01-24 12:22:00,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,666] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,666] [INFO] Running command: gunzip -c /var/lib/cwl/stga5d30306-b1bd-47eb-a15c-b55d39599bc5/GCF_000024345.1_ASM2434v1_genomic.fna.gz | prodigal -d GCF_000024345.1_ASM2434v1_genomic.fna/cds.fna -a GCF_000024345.1_ASM2434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:22,138] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:22,138] [INFO] Task started: HMMsearch
[2024-01-24 12:22:22,139] [INFO] Running command: hmmsearch --tblout GCF_000024345.1_ASM2434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/reference_markers.hmm GCF_000024345.1_ASM2434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:22,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:22,652] [INFO] Found 6/6 markers.
[2024-01-24 12:22:22,714] [INFO] Query marker FASTA was written to GCF_000024345.1_ASM2434v1_genomic.fna/markers.fasta
[2024-01-24 12:22:22,714] [INFO] Task started: Blastn
[2024-01-24 12:22:22,714] [INFO] Running command: blastn -query GCF_000024345.1_ASM2434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/reference_markers.fasta -out GCF_000024345.1_ASM2434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:24,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:24,068] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:24,069] [INFO] Target genome list was writen to GCF_000024345.1_ASM2434v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:24,078] [INFO] Task started: fastANI
[2024-01-24 12:22:24,078] [INFO] Running command: fastANI --query /var/lib/cwl/stga5d30306-b1bd-47eb-a15c-b55d39599bc5/GCF_000024345.1_ASM2434v1_genomic.fna.gz --refList GCF_000024345.1_ASM2434v1_genomic.fna/target_genomes.txt --output GCF_000024345.1_ASM2434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:51,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:51,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:51,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:51,756] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:51,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:51,757] [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 flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	100.0	2526	2526	95	conclusive
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	86.0982	1844	2526	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	84.8613	1690	2526	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	83.9215	1454	2526	95	below_threshold
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	83.6604	1643	2526	95	below_threshold
Kribbella monticola	strain=NEAU-SW521	GCA_003261635.1	2185285	2185285	type	True	83.3907	1600	2526	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	83.0157	1546	2526	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	82.882	1516	2526	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	82.7535	1433	2526	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	82.6913	1496	2526	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	82.6129	1520	2526	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	82.5773	1471	2526	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	81.9126	1373	2526	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.1484	635	2526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:51,758] [INFO] DFAST Taxonomy check result was written to GCF_000024345.1_ASM2434v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:51,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:51,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:51,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/checkm_data
[2024-01-24 12:22:51,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:51,833] [INFO] Task started: CheckM
[2024-01-24 12:22:51,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024345.1_ASM2434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024345.1_ASM2434v1_genomic.fna/checkm_input GCF_000024345.1_ASM2434v1_genomic.fna/checkm_result
[2024-01-24 12:24:28,790] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:28,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:28,817] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:28,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:28,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024345.1_ASM2434v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:28,818] [INFO] Task started: Blastn
[2024-01-24 12:24:28,818] [INFO] Running command: blastn -query GCF_000024345.1_ASM2434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg118f31e4-6e9a-40c4-a872-0511df73209b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024345.1_ASM2434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:30,801] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:30,804] [INFO] Selected 12 target genomes.
[2024-01-24 12:24:30,805] [INFO] Target genome list was writen to GCF_000024345.1_ASM2434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:30,817] [INFO] Task started: fastANI
[2024-01-24 12:24:30,817] [INFO] Running command: fastANI --query /var/lib/cwl/stga5d30306-b1bd-47eb-a15c-b55d39599bc5/GCF_000024345.1_ASM2434v1_genomic.fna.gz --refList GCF_000024345.1_ASM2434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024345.1_ASM2434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:54,976] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:54,989] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:54,989] [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_000024345.1	s__Kribbella flavida	100.0	2526	2526	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_001984195.1	s__Kribbella sp001984195	87.144	1940	2526	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	86.0855	1846	2526	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	84.8923	1684	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361855.1	s__Kribbella sp004361855	84.0772	1647	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345365.1	s__Kribbella sp004345365	83.981	1641	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.33	95.31	0.84	0.84	3	-
GCF_004348725.1	s__Kribbella sp004348725	83.9338	1452	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365175.1	s__Kribbella sp004365175	83.6334	1623	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372465.1	s__Kribbella catacumbae	83.6258	1652	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261635.1	s__Kribbella monticola	83.4323	1591	2526	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	83.3856	1588	2526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	82.9169	1511	2526	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 12:24:54,991] [INFO] GTDB search result was written to GCF_000024345.1_ASM2434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:54,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:54,994] [INFO] DFAST_QC result json was written to GCF_000024345.1_ASM2434v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:54,994] [INFO] DFAST_QC completed!
[2024-01-24 12:24:54,995] [INFO] Total running time: 0h2m56s