[2024-01-24 13:40:27,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:27,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:27,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference
[2024-01-24 13:40:29,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,027] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg5589c1ff-58f7-4b69-825f-7d57609f22e0/GCF_004354015.1_ASM435401v1_genomic.fna.gz | prodigal -d GCF_004354015.1_ASM435401v1_genomic.fna/cds.fna -a GCF_004354015.1_ASM435401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:47,629] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:47,630] [INFO] Task started: HMMsearch
[2024-01-24 13:40:47,630] [INFO] Running command: hmmsearch --tblout GCF_004354015.1_ASM435401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/reference_markers.hmm GCF_004354015.1_ASM435401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:47,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:47,979] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,024] [INFO] Query marker FASTA was written to GCF_004354015.1_ASM435401v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,024] [INFO] Task started: Blastn
[2024-01-24 13:40:48,024] [INFO] Running command: blastn -query GCF_004354015.1_ASM435401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/reference_markers.fasta -out GCF_004354015.1_ASM435401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:48,997] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,001] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:49,001] [INFO] Target genome list was writen to GCF_004354015.1_ASM435401v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,006] [INFO] Task started: fastANI
[2024-01-24 13:40:49,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg5589c1ff-58f7-4b69-825f-7d57609f22e0/GCF_004354015.1_ASM435401v1_genomic.fna.gz --refList GCF_004354015.1_ASM435401v1_genomic.fna/target_genomes.txt --output GCF_004354015.1_ASM435401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:59,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:59,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:59,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:59,590] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:59,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:59,590] [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
Arthrobacter terricola	strain=JH1-1	GCA_004354015.1	2547396	2547396	type	True	100.0	1798	1799	95	conclusive
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.9	736	1799	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	80.812	708	1799	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	80.8048	708	1799	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	80.7306	713	1799	95	below_threshold
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	80.2923	601	1799	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.2829	604	1799	95	below_threshold
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	80.256	605	1799	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.4211	403	1799	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.2755	263	1799	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.2581	264	1799	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.0911	231	1799	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.0818	233	1799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,592] [INFO] DFAST Taxonomy check result was written to GCF_004354015.1_ASM435401v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:59,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:59,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:59,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/checkm_data
[2024-01-24 13:40:59,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:59,650] [INFO] Task started: CheckM
[2024-01-24 13:40:59,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354015.1_ASM435401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354015.1_ASM435401v1_genomic.fna/checkm_input GCF_004354015.1_ASM435401v1_genomic.fna/checkm_result
[2024-01-24 13:41:50,790] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:50,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,809] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:50,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:50,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354015.1_ASM435401v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:50,809] [INFO] Task started: Blastn
[2024-01-24 13:41:50,809] [INFO] Running command: blastn -query GCF_004354015.1_ASM435401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a5dfe1-0563-4fef-9469-8f91790a4b03/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354015.1_ASM435401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,223] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:52,224] [INFO] Target genome list was writen to GCF_004354015.1_ASM435401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:52,245] [INFO] Task started: fastANI
[2024-01-24 13:41:52,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg5589c1ff-58f7-4b69-825f-7d57609f22e0/GCF_004354015.1_ASM435401v1_genomic.fna.gz --refList GCF_004354015.1_ASM435401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354015.1_ASM435401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:02,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:02,126] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:02,126] [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_004354015.1	s__Arthrobacter_K terricola	100.0	1798	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014207375.1	s__Arthrobacter_K sp014207375	82.9946	916	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002009585.1	s__Arthrobacter_K sp002009585	82.7601	941	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517125.1	s__Arthrobacter_K sp000517125	82.4639	887	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017368795.1	s__PO-11 sp017368795	81.0741	705	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	80.8969	737	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	80.8605	674	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369445.1	s__Arthrobacter_G silvisoli	80.8204	706	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	80.7443	712	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_019038615.1	s__Paenarthrobacter sp019038615	80.0491	622	1799	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,128] [INFO] GTDB search result was written to GCF_004354015.1_ASM435401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:02,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:02,131] [INFO] DFAST_QC result json was written to GCF_004354015.1_ASM435401v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:02,131] [INFO] DFAST_QC completed!
[2024-01-24 13:42:02,131] [INFO] Total running time: 0h1m35s