[2024-01-25 20:05:20,646] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,647] [INFO] DQC Reference Directory: /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference
[2024-01-25 20:05:21,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,744] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg46ceb6f5-e4a4-43b3-b7f1-a3af865eafa9/GCF_900445045.1_49888_F01_genomic.fna.gz | prodigal -d GCF_900445045.1_49888_F01_genomic.fna/cds.fna -a GCF_900445045.1_49888_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:29,090] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:29,090] [INFO] Task started: HMMsearch
[2024-01-25 20:05:29,090] [INFO] Running command: hmmsearch --tblout GCF_900445045.1_49888_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/reference_markers.hmm GCF_900445045.1_49888_F01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:29,299] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:29,300] [INFO] Found 6/6 markers.
[2024-01-25 20:05:29,324] [INFO] Query marker FASTA was written to GCF_900445045.1_49888_F01_genomic.fna/markers.fasta
[2024-01-25 20:05:29,324] [INFO] Task started: Blastn
[2024-01-25 20:05:29,324] [INFO] Running command: blastn -query GCF_900445045.1_49888_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/reference_markers.fasta -out GCF_900445045.1_49888_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:30,522] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:30,527] [INFO] Selected 11 target genomes.
[2024-01-25 20:05:30,527] [INFO] Target genome list was writen to GCF_900445045.1_49888_F01_genomic.fna/target_genomes.txt
[2024-01-25 20:05:30,583] [INFO] Task started: fastANI
[2024-01-25 20:05:30,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ceb6f5-e4a4-43b3-b7f1-a3af865eafa9/GCF_900445045.1_49888_F01_genomic.fna.gz --refList GCF_900445045.1_49888_F01_genomic.fna/target_genomes.txt --output GCF_900445045.1_49888_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:38,100] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:38,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:38,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:38,108] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:05:38,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:38,108] [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 denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	100.0	956	958	95	conclusive
Actinomyces denticolens	strain=DSM 20671	GCA_001995055.1	52767	52767	type	True	99.9815	954	958	95	conclusive
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	99.9344	892	958	95	conclusive
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	92.0333	662	958	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_013177295.1	2737173	2737173	type	True	92.02	733	958	95	below_threshold
Actinomyces gaoshouyii	strain=pika_113	GCA_002072175.1	1960083	1960083	type	True	91.9413	708	958	95	below_threshold
Actinomyces gaoshouyii	strain=CGMCC 4.7372	GCA_014646495.1	1960083	1960083	type	True	91.8626	719	958	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	90.4191	797	958	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	78.0741	281	958	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.8826	303	958	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.9693	199	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:38,110] [INFO] DFAST Taxonomy check result was written to GCF_900445045.1_49888_F01_genomic.fna/tc_result.tsv
[2024-01-25 20:05:38,110] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:38,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:38,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/checkm_data
[2024-01-25 20:05:38,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:38,141] [INFO] Task started: CheckM
[2024-01-25 20:05:38,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445045.1_49888_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445045.1_49888_F01_genomic.fna/checkm_input GCF_900445045.1_49888_F01_genomic.fna/checkm_result
[2024-01-25 20:06:09,260] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:09,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:09,277] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:09,277] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:09,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445045.1_49888_F01_genomic.fna/markers.fasta)
[2024-01-25 20:06:09,279] [INFO] Task started: Blastn
[2024-01-25 20:06:09,279] [INFO] Running command: blastn -query GCF_900445045.1_49888_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stge5af5cf0-cf06-42e1-8405-fb129719dd05/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445045.1_49888_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:11,350] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:11,353] [INFO] Selected 9 target genomes.
[2024-01-25 20:06:11,353] [INFO] Target genome list was writen to GCF_900445045.1_49888_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:11,378] [INFO] Task started: fastANI
[2024-01-25 20:06:11,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ceb6f5-e4a4-43b3-b7f1-a3af865eafa9/GCF_900445045.1_49888_F01_genomic.fna.gz --refList GCF_900445045.1_49888_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445045.1_49888_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:18,372] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:18,379] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:18,379] [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_002072185.1	s__Actinomyces denticolens	99.9344	892	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	conclusive
GCF_013177295.1	s__Actinomyces marmotae	91.9964	734	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.20	98.86	0.98	0.97	5	-
GCF_002072175.1	s__Actinomyces gaoshouyii	91.9662	707	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.77	99.54	0.99	0.99	3	-
GCF_000295095.1	s__Actinomyces timonensis	90.399	798	958	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	81.6142	546	958	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	81.4503	533	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCA_000711965.1	s__Actinomyces israelii	81.3528	556	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_006546825.1	s__Actinomyces oris	81.3502	513	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_900637165.1	s__Actinomyces howellii	81.1809	492	958	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:18,385] [INFO] GTDB search result was written to GCF_900445045.1_49888_F01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:18,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:18,388] [INFO] DFAST_QC result json was written to GCF_900445045.1_49888_F01_genomic.fna/dqc_result.json
[2024-01-25 20:06:18,388] [INFO] DFAST_QC completed!
[2024-01-25 20:06:18,388] [INFO] Total running time: 0h0m58s