[2024-01-24 13:41:40,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference
[2024-01-24 13:41:42,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,006] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,006] [INFO] Running command: gunzip -c /var/lib/cwl/stge6e5c6c8-2bb7-4b43-9ac7-12022a4d1a30/GCF_009829655.1_ASM982965v1_genomic.fna.gz | prodigal -d GCF_009829655.1_ASM982965v1_genomic.fna/cds.fna -a GCF_009829655.1_ASM982965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:48,656] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:48,657] [INFO] Task started: HMMsearch
[2024-01-24 13:41:48,657] [INFO] Running command: hmmsearch --tblout GCF_009829655.1_ASM982965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/reference_markers.hmm GCF_009829655.1_ASM982965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:48,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:48,894] [INFO] Found 6/6 markers.
[2024-01-24 13:41:48,920] [INFO] Query marker FASTA was written to GCF_009829655.1_ASM982965v1_genomic.fna/markers.fasta
[2024-01-24 13:41:48,920] [INFO] Task started: Blastn
[2024-01-24 13:41:48,921] [INFO] Running command: blastn -query GCF_009829655.1_ASM982965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/reference_markers.fasta -out GCF_009829655.1_ASM982965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:49,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:49,927] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:49,928] [INFO] Target genome list was writen to GCF_009829655.1_ASM982965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:49,934] [INFO] Task started: fastANI
[2024-01-24 13:41:49,934] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e5c6c8-2bb7-4b43-9ac7-12022a4d1a30/GCF_009829655.1_ASM982965v1_genomic.fna.gz --refList GCF_009829655.1_ASM982965v1_genomic.fna/target_genomes.txt --output GCF_009829655.1_ASM982965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:56,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:56,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:56,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:56,477] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:56,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:56,477] [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
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	100.0	726	730	95	conclusive
Actinomyces marmotae	strain=zg-325	GCA_013177295.1	2737173	2737173	type	True	99.9982	728	730	95	conclusive
Actinomyces gaoshouyii	strain=CGMCC 4.7372	GCA_014646495.1	1960083	1960083	type	True	92.6296	626	730	95	below_threshold
Actinomyces gaoshouyii	strain=pika_113	GCA_002072175.1	1960083	1960083	type	True	92.6049	618	730	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	92.1804	631	730	95	below_threshold
Actinomyces denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	92.0847	658	730	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_001995055.1	52767	52767	type	True	92.0765	661	730	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	89.49	629	730	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.9947	241	730	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	77.3202	157	730	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	77.2398	161	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,479] [INFO] DFAST Taxonomy check result was written to GCF_009829655.1_ASM982965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:56,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:56,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:56,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/checkm_data
[2024-01-24 13:41:56,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:56,507] [INFO] Task started: CheckM
[2024-01-24 13:41:56,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009829655.1_ASM982965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009829655.1_ASM982965v1_genomic.fna/checkm_input GCF_009829655.1_ASM982965v1_genomic.fna/checkm_result
[2024-01-24 13:42:21,893] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:21,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,913] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:21,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:21,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009829655.1_ASM982965v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:21,914] [INFO] Task started: Blastn
[2024-01-24 13:42:21,915] [INFO] Running command: blastn -query GCF_009829655.1_ASM982965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6776a41e-9051-43fa-acbf-ea0e62fb1e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_009829655.1_ASM982965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:23,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:23,566] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:23,567] [INFO] Target genome list was writen to GCF_009829655.1_ASM982965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:23,606] [INFO] Task started: fastANI
[2024-01-24 13:42:23,606] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e5c6c8-2bb7-4b43-9ac7-12022a4d1a30/GCF_009829655.1_ASM982965v1_genomic.fna.gz --refList GCF_009829655.1_ASM982965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009829655.1_ASM982965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:28,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:28,489] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:28,489] [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_013177295.1	s__Actinomyces marmotae	99.9982	728	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.20	98.86	0.98	0.97	5	conclusive
GCF_002072175.1	s__Actinomyces gaoshouyii	92.6049	618	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.77	99.54	0.99	0.99	3	-
GCF_002072185.1	s__Actinomyces denticolens	92.1396	633	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	-
GCF_000295095.1	s__Actinomyces timonensis	89.4809	630	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553565.1	s__Actinomyces radicidentis	81.8003	445	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429225.1	s__Actinomyces dentalis	81.5091	439	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_006546825.1	s__Actinomyces oris	81.2072	443	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:28,491] [INFO] GTDB search result was written to GCF_009829655.1_ASM982965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:28,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:28,498] [INFO] DFAST_QC result json was written to GCF_009829655.1_ASM982965v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:28,498] [INFO] DFAST_QC completed!
[2024-01-24 13:42:28,499] [INFO] Total running time: 0h0m48s