[2024-01-24 13:21:40,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference
[2024-01-24 13:21:41,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:41,946] [INFO] Task started: Prodigal
[2024-01-24 13:21:41,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg19c3ffe6-fe32-4e94-b9c9-9cdf3680129c/GCF_004217145.1_ASM421714v1_genomic.fna.gz | prodigal -d GCF_004217145.1_ASM421714v1_genomic.fna/cds.fna -a GCF_004217145.1_ASM421714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,576] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,576] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,576] [INFO] Running command: hmmsearch --tblout GCF_004217145.1_ASM421714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/reference_markers.hmm GCF_004217145.1_ASM421714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,070] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,142] [INFO] Query marker FASTA was written to GCF_004217145.1_ASM421714v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,143] [INFO] Task started: Blastn
[2024-01-24 13:22:09,143] [INFO] Running command: blastn -query GCF_004217145.1_ASM421714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/reference_markers.fasta -out GCF_004217145.1_ASM421714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,483] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,486] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:10,487] [INFO] Target genome list was writen to GCF_004217145.1_ASM421714v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,493] [INFO] Task started: fastANI
[2024-01-24 13:22:10,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c3ffe6-fe32-4e94-b9c9-9cdf3680129c/GCF_004217145.1_ASM421714v1_genomic.fna.gz --refList GCF_004217145.1_ASM421714v1_genomic.fna/target_genomes.txt --output GCF_004217145.1_ASM421714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:40,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:40,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:40,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:40,445] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:40,445] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:40,446] [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	91.4966	2408	2868	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	86.9775	2183	2868	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	86.914	2148	2868	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	86.7395	2112	2868	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	86.3699	1996	2868	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	86.1379	1989	2868	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	85.9529	1999	2868	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	85.0177	1801	2868	95	below_threshold
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	84.6637	1973	2868	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	84.4843	2009	2868	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	84.0811	1586	2868	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	82.9238	1589	2868	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	82.9219	1598	2868	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	77.0676	450	2868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,449] [INFO] DFAST Taxonomy check result was written to GCF_004217145.1_ASM421714v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:40,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:40,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:40,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/checkm_data
[2024-01-24 13:22:40,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:40,537] [INFO] Task started: CheckM
[2024-01-24 13:22:40,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217145.1_ASM421714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217145.1_ASM421714v1_genomic.fna/checkm_input GCF_004217145.1_ASM421714v1_genomic.fna/checkm_result
[2024-01-24 13:23:54,857] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:54,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:54,882] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:54,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:54,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217145.1_ASM421714v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:54,883] [INFO] Task started: Blastn
[2024-01-24 13:23:54,883] [INFO] Running command: blastn -query GCF_004217145.1_ASM421714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a8bfb2-a623-4d1d-b4a3-32317e4094da/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217145.1_ASM421714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:56,742] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:56,745] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:56,745] [INFO] Target genome list was writen to GCF_004217145.1_ASM421714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:56,761] [INFO] Task started: fastANI
[2024-01-24 13:23:56,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c3ffe6-fe32-4e94-b9c9-9cdf3680129c/GCF_004217145.1_ASM421714v1_genomic.fna.gz --refList GCF_004217145.1_ASM421714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217145.1_ASM421714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:20,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:20,940] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:20,940] [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_004217145.1	s__Kribbella soli_A	100.0	2866	2868	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_004365355.1	s__Kribbella sp004365355	92.5428	2398	2868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	91.4871	2407	2868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	88.068	2238	2868	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	86.9769	2182	2868	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	86.8093	2121	2868	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	86.7468	2110	2868	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	86.3661	1997	2868	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	86.1403	1989	2868	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715085.1	s__Kribbella jejuensis	85.9493	1998	2868	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	84.0895	1933	2868	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 13:24:20,942] [INFO] GTDB search result was written to GCF_004217145.1_ASM421714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:20,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:20,945] [INFO] DFAST_QC result json was written to GCF_004217145.1_ASM421714v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:20,945] [INFO] DFAST_QC completed!
[2024-01-24 13:24:20,946] [INFO] Total running time: 0h2m40s