[2024-01-25 17:46:05,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference
[2024-01-25 17:46:06,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:06,993] [INFO] Task started: Prodigal
[2024-01-25 17:46:06,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg8573ebad-8de2-4f92-836d-83143eb99a8d/GCF_009377195.2_ASM937719v2_genomic.fna.gz | prodigal -d GCF_009377195.2_ASM937719v2_genomic.fna/cds.fna -a GCF_009377195.2_ASM937719v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:16,244] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:16,245] [INFO] Task started: HMMsearch
[2024-01-25 17:46:16,245] [INFO] Running command: hmmsearch --tblout GCF_009377195.2_ASM937719v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/reference_markers.hmm GCF_009377195.2_ASM937719v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:16,503] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:16,504] [INFO] Found 6/6 markers.
[2024-01-25 17:46:16,535] [INFO] Query marker FASTA was written to GCF_009377195.2_ASM937719v2_genomic.fna/markers.fasta
[2024-01-25 17:46:16,535] [INFO] Task started: Blastn
[2024-01-25 17:46:16,535] [INFO] Running command: blastn -query GCF_009377195.2_ASM937719v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/reference_markers.fasta -out GCF_009377195.2_ASM937719v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:17,621] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:17,628] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:17,628] [INFO] Target genome list was writen to GCF_009377195.2_ASM937719v2_genomic.fna/target_genomes.txt
[2024-01-25 17:46:17,632] [INFO] Task started: fastANI
[2024-01-25 17:46:17,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg8573ebad-8de2-4f92-836d-83143eb99a8d/GCF_009377195.2_ASM937719v2_genomic.fna.gz --refList GCF_009377195.2_ASM937719v2_genomic.fna/target_genomes.txt --output GCF_009377195.2_ASM937719v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:26,568] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:26,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:26,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:26,575] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:26,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:26,576] [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 bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	100.0	1200	1201	95	conclusive
Arthrobacter agilis	strain=DSM 20550	GCA_006494655.1	37921	37921	type	True	84.3936	849	1201	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	83.5964	829	1201	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	83.546	822	1201	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	83.504	871	1201	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	83.1941	807	1201	95	below_threshold
Arthrobacter zhaoguopingii	strain=J391	GCA_009828595.1	2681491	2681491	type	True	80.1381	530	1201	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2596	350	1201	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.2267	369	1201	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.1891	360	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:26,577] [INFO] DFAST Taxonomy check result was written to GCF_009377195.2_ASM937719v2_genomic.fna/tc_result.tsv
[2024-01-25 17:46:26,578] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:26,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:26,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/checkm_data
[2024-01-25 17:46:26,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:26,616] [INFO] Task started: CheckM
[2024-01-25 17:46:26,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377195.2_ASM937719v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377195.2_ASM937719v2_genomic.fna/checkm_input GCF_009377195.2_ASM937719v2_genomic.fna/checkm_result
[2024-01-25 17:46:59,850] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:59,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:59,868] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:59,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:59,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377195.2_ASM937719v2_genomic.fna/markers.fasta)
[2024-01-25 17:46:59,869] [INFO] Task started: Blastn
[2024-01-25 17:46:59,869] [INFO] Running command: blastn -query GCF_009377195.2_ASM937719v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga1a4577f-5da3-4a15-85f5-4e549fdf641a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377195.2_ASM937719v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:01,666] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:01,668] [INFO] Selected 11 target genomes.
[2024-01-25 17:47:01,668] [INFO] Target genome list was writen to GCF_009377195.2_ASM937719v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:01,679] [INFO] Task started: fastANI
[2024-01-25 17:47:01,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg8573ebad-8de2-4f92-836d-83143eb99a8d/GCF_009377195.2_ASM937719v2_genomic.fna.gz --refList GCF_009377195.2_ASM937719v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009377195.2_ASM937719v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:11,863] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:11,871] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:11,871] [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_009377195.2	s__Arthrobacter_D bussei	100.0	1200	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.3875	N/A	N/A	N/A	N/A	1	conclusive
GCF_001422665.1	s__Arthrobacter_D sp001422665	95.3771	1050	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.3875	N/A	N/A	N/A	N/A	1	-
GCF_006494655.1	s__Arthrobacter_D agilis	84.3936	849	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	100.00	100.00	1.00	1.00	4	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	83.7796	871	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816565.1	s__Arthrobacter_D sp000816565	83.7228	817	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954225.1	s__Arthrobacter_D ruber	83.5964	829	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002927275.1	s__Arthrobacter_D pityocampae	83.557	821	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602275.1	s__Arthrobacter_D sp003602275	83.5008	872	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929295.1	s__Arthrobacter_D sp002929295	83.391	822	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752045.1	s__Arthrobacter_D sp015752045	83.3044	810	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157505.1	s__Arthrobacter_D agilis_D	83.2639	799	1201	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:11,872] [INFO] GTDB search result was written to GCF_009377195.2_ASM937719v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:11,873] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:11,875] [INFO] DFAST_QC result json was written to GCF_009377195.2_ASM937719v2_genomic.fna/dqc_result.json
[2024-01-25 17:47:11,876] [INFO] DFAST_QC completed!
[2024-01-25 17:47:11,876] [INFO] Total running time: 0h1m6s