[2024-01-24 12:54:05,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,693] [INFO] DQC Reference Directory: /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference
[2024-01-24 12:54:07,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,725] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cbdf23f-01cd-4605-b422-22f24f98769d/GCF_000295095.1_ASM29509v1_genomic.fna.gz | prodigal -d GCF_000295095.1_ASM29509v1_genomic.fna/cds.fna -a GCF_000295095.1_ASM29509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:16,451] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:16,451] [INFO] Task started: HMMsearch
[2024-01-24 12:54:16,452] [INFO] Running command: hmmsearch --tblout GCF_000295095.1_ASM29509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/reference_markers.hmm GCF_000295095.1_ASM29509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:16,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:16,783] [INFO] Found 6/6 markers.
[2024-01-24 12:54:16,809] [INFO] Query marker FASTA was written to GCF_000295095.1_ASM29509v1_genomic.fna/markers.fasta
[2024-01-24 12:54:16,809] [INFO] Task started: Blastn
[2024-01-24 12:54:16,809] [INFO] Running command: blastn -query GCF_000295095.1_ASM29509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/reference_markers.fasta -out GCF_000295095.1_ASM29509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:18,095] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:18,099] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:18,100] [INFO] Target genome list was writen to GCF_000295095.1_ASM29509v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:18,117] [INFO] Task started: fastANI
[2024-01-24 12:54:18,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cbdf23f-01cd-4605-b422-22f24f98769d/GCF_000295095.1_ASM29509v1_genomic.fna.gz --refList GCF_000295095.1_ASM29509v1_genomic.fna/target_genomes.txt --output GCF_000295095.1_ASM29509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:25,511] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:25,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:25,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:25,521] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:25,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:25,522] [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 timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	99.9999	973	975	95	conclusive
Actinomyces denticolens	strain=DSM 20671	GCA_001995055.1	52767	52767	type	True	90.3637	797	975	95	below_threshold
Actinomyces denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	90.3221	810	975	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	90.2831	758	975	95	below_threshold
Actinomyces gaoshouyii	strain=CGMCC 4.7372	GCA_014646495.1	1960083	1960083	type	True	89.3227	698	975	95	below_threshold
Actinomyces gaoshouyii	strain=pika_113	GCA_002072175.1	1960083	1960083	type	True	89.3096	692	975	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	89.2134	645	975	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.1462	308	975	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.7796	322	975	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.0904	192	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,524] [INFO] DFAST Taxonomy check result was written to GCF_000295095.1_ASM29509v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:25,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:25,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:25,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/checkm_data
[2024-01-24 12:54:25,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:25,560] [INFO] Task started: CheckM
[2024-01-24 12:54:25,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000295095.1_ASM29509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000295095.1_ASM29509v1_genomic.fna/checkm_input GCF_000295095.1_ASM29509v1_genomic.fna/checkm_result
[2024-01-24 12:55:00,955] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:00,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:00,977] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:00,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:00,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000295095.1_ASM29509v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:00,978] [INFO] Task started: Blastn
[2024-01-24 12:55:00,978] [INFO] Running command: blastn -query GCF_000295095.1_ASM29509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e45d95-bf2c-467b-b889-f065a27b7bba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000295095.1_ASM29509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:03,194] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:03,201] [INFO] Selected 7 target genomes.
[2024-01-24 12:55:03,201] [INFO] Target genome list was writen to GCF_000295095.1_ASM29509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:03,209] [INFO] Task started: fastANI
[2024-01-24 12:55:03,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cbdf23f-01cd-4605-b422-22f24f98769d/GCF_000295095.1_ASM29509v1_genomic.fna.gz --refList GCF_000295095.1_ASM29509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000295095.1_ASM29509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:08,687] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:08,701] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:08,702] [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_000295095.1	s__Actinomyces timonensis	99.9999	973	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002072185.1	s__Actinomyces denticolens	90.2831	758	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	-
GCF_002072175.1	s__Actinomyces gaoshouyii	89.3096	692	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.77	99.54	0.99	0.99	3	-
GCF_013177295.1	s__Actinomyces marmotae	89.1734	716	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.20	98.86	0.98	0.97	5	-
GCF_001929375.1	s__Actinomyces oris_B	82.27	511	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_001553565.1	s__Actinomyces radicidentis	82.1662	545	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000711965.1	s__Actinomyces israelii	81.413	570	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:08,703] [INFO] GTDB search result was written to GCF_000295095.1_ASM29509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:08,704] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:08,707] [INFO] DFAST_QC result json was written to GCF_000295095.1_ASM29509v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:08,708] [INFO] DFAST_QC completed!
[2024-01-24 12:55:08,708] [INFO] Total running time: 0h1m3s