[2024-01-24 13:21:42,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:42,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:42,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference
[2024-01-24 13:21:44,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:44,216] [INFO] Task started: Prodigal
[2024-01-24 13:21:44,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a832ebb-afd9-4f7f-9eec-26ed5fe828db/GCF_006494655.1_ASM649465v1_genomic.fna.gz | prodigal -d GCF_006494655.1_ASM649465v1_genomic.fna/cds.fna -a GCF_006494655.1_ASM649465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:53,825] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:53,826] [INFO] Task started: HMMsearch
[2024-01-24 13:21:53,826] [INFO] Running command: hmmsearch --tblout GCF_006494655.1_ASM649465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/reference_markers.hmm GCF_006494655.1_ASM649465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:54,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:54,124] [INFO] Found 6/6 markers.
[2024-01-24 13:21:54,162] [INFO] Query marker FASTA was written to GCF_006494655.1_ASM649465v1_genomic.fna/markers.fasta
[2024-01-24 13:21:54,162] [INFO] Task started: Blastn
[2024-01-24 13:21:54,162] [INFO] Running command: blastn -query GCF_006494655.1_ASM649465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/reference_markers.fasta -out GCF_006494655.1_ASM649465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:55,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:55,324] [INFO] Selected 10 target genomes.
[2024-01-24 13:21:55,324] [INFO] Target genome list was writen to GCF_006494655.1_ASM649465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:55,327] [INFO] Task started: fastANI
[2024-01-24 13:21:55,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a832ebb-afd9-4f7f-9eec-26ed5fe828db/GCF_006494655.1_ASM649465v1_genomic.fna.gz --refList GCF_006494655.1_ASM649465v1_genomic.fna/target_genomes.txt --output GCF_006494655.1_ASM649465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:03,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:03,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:03,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:03,582] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:03,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:03,582] [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 agilis	strain=DSM 20550	GCA_006494655.1	37921	37921	type	True	100.0	1061	1065	95	conclusive
Arthrobacter bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	84.6722	830	1065	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	83.1618	761	1065	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	83.1503	781	1065	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	82.9371	768	1065	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	82.9298	750	1065	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	79.7784	506	1065	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.3372	319	1065	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.2053	278	1065	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.1694	278	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:03,584] [INFO] DFAST Taxonomy check result was written to GCF_006494655.1_ASM649465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:03,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:03,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:03,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/checkm_data
[2024-01-24 13:22:03,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:03,624] [INFO] Task started: CheckM
[2024-01-24 13:22:03,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006494655.1_ASM649465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006494655.1_ASM649465v1_genomic.fna/checkm_input GCF_006494655.1_ASM649465v1_genomic.fna/checkm_result
[2024-01-24 13:22:37,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:37,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:37,092] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:37,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:37,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006494655.1_ASM649465v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:37,094] [INFO] Task started: Blastn
[2024-01-24 13:22:37,094] [INFO] Running command: blastn -query GCF_006494655.1_ASM649465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b49847d-07df-4520-896e-60d168eda9ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_006494655.1_ASM649465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:38,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:38,896] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:38,896] [INFO] Target genome list was writen to GCF_006494655.1_ASM649465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:38,908] [INFO] Task started: fastANI
[2024-01-24 13:22:38,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a832ebb-afd9-4f7f-9eec-26ed5fe828db/GCF_006494655.1_ASM649465v1_genomic.fna.gz --refList GCF_006494655.1_ASM649465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006494655.1_ASM649465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:49,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:49,783] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:49,783] [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_006494655.1	s__Arthrobacter_D agilis	100.0	1061	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_009377195.2	s__Arthrobacter_D bussei	84.6598	831	1065	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_001422665.1	s__Arthrobacter_D sp001422665	84.4995	812	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.3875	N/A	N/A	N/A	N/A	1	-
GCA_004001285.1	s__Arthrobacter_D sp004001285	83.3887	814	1065	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	83.3409	782	1065	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_002929375.1	s__Arthrobacter_D sp002929375	83.2868	785	1065	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	83.2234	773	1065	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	83.1581	780	1065	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_002929355.1	s__Arthrobacter_D sp002929355	83.0778	774	1065	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	83.066	744	1065	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	82.9913	749	1065	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	82.9316	768	1065	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_001187915.1	s__Arthrobacter_D sp001187915	82.269	654	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:49,789] [INFO] GTDB search result was written to GCF_006494655.1_ASM649465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:49,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:49,794] [INFO] DFAST_QC result json was written to GCF_006494655.1_ASM649465v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:49,795] [INFO] DFAST_QC completed!
[2024-01-24 13:22:49,795] [INFO] Total running time: 0h1m7s