[2024-01-24 14:31:14,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference
[2024-01-24 14:31:15,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,515] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg976b0cc6-24c2-435b-beb9-0a18d28f8e91/GCF_005298075.1_ASM529807v1_genomic.fna.gz | prodigal -d GCF_005298075.1_ASM529807v1_genomic.fna/cds.fna -a GCF_005298075.1_ASM529807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:30,140] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:30,140] [INFO] Task started: HMMsearch
[2024-01-24 14:31:30,140] [INFO] Running command: hmmsearch --tblout GCF_005298075.1_ASM529807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/reference_markers.hmm GCF_005298075.1_ASM529807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:30,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:30,496] [INFO] Found 6/6 markers.
[2024-01-24 14:31:30,541] [INFO] Query marker FASTA was written to GCF_005298075.1_ASM529807v1_genomic.fna/markers.fasta
[2024-01-24 14:31:30,541] [INFO] Task started: Blastn
[2024-01-24 14:31:30,541] [INFO] Running command: blastn -query GCF_005298075.1_ASM529807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/reference_markers.fasta -out GCF_005298075.1_ASM529807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:31,806] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:31,810] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:31,811] [INFO] Target genome list was writen to GCF_005298075.1_ASM529807v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:31,819] [INFO] Task started: fastANI
[2024-01-24 14:31:31,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg976b0cc6-24c2-435b-beb9-0a18d28f8e91/GCF_005298075.1_ASM529807v1_genomic.fna.gz --refList GCF_005298075.1_ASM529807v1_genomic.fna/target_genomes.txt --output GCF_005298075.1_ASM529807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:45,823] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:45,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:45,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:45,835] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:45,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:45,835] [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
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	100.0	1605	1606	95	conclusive
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	79.833	796	1606	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	79.2909	631	1606	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	79.0601	615	1606	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.5914	552	1606	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	78.5028	620	1606	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	77.7	474	1606	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	77.2559	368	1606	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	76.9924	378	1606	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	76.3093	380	1606	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	76.197	339	1606	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	76.0417	511	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,837] [INFO] DFAST Taxonomy check result was written to GCF_005298075.1_ASM529807v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:45,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:45,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:45,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/checkm_data
[2024-01-24 14:31:45,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:45,887] [INFO] Task started: CheckM
[2024-01-24 14:31:45,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005298075.1_ASM529807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005298075.1_ASM529807v1_genomic.fna/checkm_input GCF_005298075.1_ASM529807v1_genomic.fna/checkm_result
[2024-01-24 14:33:01,626] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:01,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:01,652] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:01,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:01,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005298075.1_ASM529807v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:01,653] [INFO] Task started: Blastn
[2024-01-24 14:33:01,653] [INFO] Running command: blastn -query GCF_005298075.1_ASM529807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78beb754-225e-4eae-90c1-e77f3efe5379/dqc_reference/reference_markers_gtdb.fasta -out GCF_005298075.1_ASM529807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:03,418] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:03,421] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:03,421] [INFO] Target genome list was writen to GCF_005298075.1_ASM529807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:03,430] [INFO] Task started: fastANI
[2024-01-24 14:33:03,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg976b0cc6-24c2-435b-beb9-0a18d28f8e91/GCF_005298075.1_ASM529807v1_genomic.fna.gz --refList GCF_005298075.1_ASM529807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005298075.1_ASM529807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:18,540] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:18,557] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:18,557] [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_005298075.1	s__Nakamurella flava	100.0	1605	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024365.1	s__Nakamurella multipartita	79.84	794	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918095.1	s__Nakamurella flavida	79.232	637	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918035.1	s__Nakamurella sp016918035	79.047	616	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707545.1	s__Nakamurella sp009707545	78.841	624	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260015.1	s__Nakamurella deserti	78.56	556	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646215.1	s__Nakamurella endophytica	78.4965	621	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104535.1	s__Nakamurella panacisegetis	78.3819	493	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882715.1	s__Nakamurella sp017882715	78.1587	446	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426645.1	s__Nakamurella lactea	77.686	476	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016526145.1	s__Saccharopolyspora_C sp016526145	76.7081	366	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362825.1	s__Labedaea rhizosphaerae	76.637	457	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016342265.1	s__Corynebacterium sp016342265	76.4019	108	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295035.1	s__Streptomyces buecherae	76.2939	383	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:18,559] [INFO] GTDB search result was written to GCF_005298075.1_ASM529807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:18,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:18,564] [INFO] DFAST_QC result json was written to GCF_005298075.1_ASM529807v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:18,564] [INFO] DFAST_QC completed!
[2024-01-24 14:33:18,564] [INFO] Total running time: 0h2m4s