[2024-01-24 10:47:40,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,787] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,787] [INFO] Running command: gunzip -c /var/lib/cwl/stgb63ea8dc-b32c-4c79-9075-d95b4ab581cd/GCF_002259645.1_ASM225964v1_genomic.fna.gz | prodigal -d GCF_002259645.1_ASM225964v1_genomic.fna/cds.fna -a GCF_002259645.1_ASM225964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:54,259] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:54,260] [INFO] Task started: HMMsearch
[2024-01-24 10:47:54,260] [INFO] Running command: hmmsearch --tblout GCF_002259645.1_ASM225964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/reference_markers.hmm GCF_002259645.1_ASM225964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:54,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:54,506] [INFO] Found 6/6 markers.
[2024-01-24 10:47:54,536] [INFO] Query marker FASTA was written to GCF_002259645.1_ASM225964v1_genomic.fna/markers.fasta
[2024-01-24 10:47:54,537] [INFO] Task started: Blastn
[2024-01-24 10:47:54,537] [INFO] Running command: blastn -query GCF_002259645.1_ASM225964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/reference_markers.fasta -out GCF_002259645.1_ASM225964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:55,423] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:55,427] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:55,428] [INFO] Target genome list was writen to GCF_002259645.1_ASM225964v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:55,432] [INFO] Task started: fastANI
[2024-01-24 10:47:55,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgb63ea8dc-b32c-4c79-9075-d95b4ab581cd/GCF_002259645.1_ASM225964v1_genomic.fna.gz --refList GCF_002259645.1_ASM225964v1_genomic.fna/target_genomes.txt --output GCF_002259645.1_ASM225964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:04,613] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:04,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:04,631] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:04,632] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:04,632] [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
Bifidobacterium tissieri	strain=DSM 100201	GCA_002259645.1	1630162	1630162	type	True	100.0	938	940	95	conclusive
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	87.5029	741	940	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	87.4565	727	940	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	83.3317	535	940	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	83.2846	533	940	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	82.9409	535	940	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	82.618	504	940	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.7076	359	940	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	80.6717	362	940	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	80.3617	366	940	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	76.2656	71	940	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	76.2509	75	940	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	75.6817	60	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,633] [INFO] DFAST Taxonomy check result was written to GCF_002259645.1_ASM225964v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:04,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:04,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:04,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/checkm_data
[2024-01-24 10:48:04,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:04,668] [INFO] Task started: CheckM
[2024-01-24 10:48:04,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259645.1_ASM225964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259645.1_ASM225964v1_genomic.fna/checkm_input GCF_002259645.1_ASM225964v1_genomic.fna/checkm_result
[2024-01-24 10:48:38,074] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:38,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:38,100] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:38,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:38,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259645.1_ASM225964v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:38,101] [INFO] Task started: Blastn
[2024-01-24 10:48:38,101] [INFO] Running command: blastn -query GCF_002259645.1_ASM225964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48d38333-3d55-44cd-8106-aea74b39457f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259645.1_ASM225964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:39,294] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:39,297] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:39,298] [INFO] Target genome list was writen to GCF_002259645.1_ASM225964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:39,302] [INFO] Task started: fastANI
[2024-01-24 10:48:39,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgb63ea8dc-b32c-4c79-9075-d95b4ab581cd/GCF_002259645.1_ASM225964v1_genomic.fna.gz --refList GCF_002259645.1_ASM225964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259645.1_ASM225964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:45,004] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:45,012] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:45,012] [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_002259645.1	s__Galliscardovia tissieri	100.0	938	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	conclusive
GCF_002234915.1	s__Galliscardovia vansinderenii	87.5029	741	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	87.4565	727	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	83.3282	537	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002802875.1	s__Galliscardovia primatium	83.2846	533	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129925.1	s__Galliscardovia catulorum	82.6822	500	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	82.618	504	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_009299505.1	s__Bifidobacterium ramosum	80.5435	360	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	80.3615	366	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,014] [INFO] GTDB search result was written to GCF_002259645.1_ASM225964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:45,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:45,018] [INFO] DFAST_QC result json was written to GCF_002259645.1_ASM225964v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:45,018] [INFO] DFAST_QC completed!
[2024-01-24 10:48:45,018] [INFO] Total running time: 0h1m4s