[2023-06-28 10:15:48,111] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:15:48,119] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:15:48,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference
[2023-06-28 10:15:49,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:15:49,410] [INFO] Task started: Prodigal
[2023-06-28 10:15:49,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg5826f1d2-2fc2-4399-8971-d159d48e1711/GCA_017652165.1_ASM1765216v1_genomic.fna.gz | prodigal -d GCA_017652165.1_ASM1765216v1_genomic.fna/cds.fna -a GCA_017652165.1_ASM1765216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:15:52,534] [INFO] Task succeeded: Prodigal
[2023-06-28 10:15:52,534] [INFO] Task started: HMMsearch
[2023-06-28 10:15:52,534] [INFO] Running command: hmmsearch --tblout GCA_017652165.1_ASM1765216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/reference_markers.hmm GCA_017652165.1_ASM1765216v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:15:52,729] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:15:52,731] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5826f1d2-2fc2-4399-8971-d159d48e1711/GCA_017652165.1_ASM1765216v1_genomic.fna.gz]
[2023-06-28 10:15:52,746] [INFO] Query marker FASTA was written to GCA_017652165.1_ASM1765216v1_genomic.fna/markers.fasta
[2023-06-28 10:15:52,746] [INFO] Task started: Blastn
[2023-06-28 10:15:52,746] [INFO] Running command: blastn -query GCA_017652165.1_ASM1765216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/reference_markers.fasta -out GCA_017652165.1_ASM1765216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:15:54,307] [INFO] Task succeeded: Blastn
[2023-06-28 10:15:54,311] [INFO] Selected 22 target genomes.
[2023-06-28 10:15:54,311] [INFO] Target genome list was writen to GCA_017652165.1_ASM1765216v1_genomic.fna/target_genomes.txt
[2023-06-28 10:15:54,314] [INFO] Task started: fastANI
[2023-06-28 10:15:54,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5826f1d2-2fc2-4399-8971-d159d48e1711/GCA_017652165.1_ASM1765216v1_genomic.fna.gz --refList GCA_017652165.1_ASM1765216v1_genomic.fna/target_genomes.txt --output GCA_017652165.1_ASM1765216v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:02,959] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:02,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:02,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:02,973] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:02,974] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:16:02,974] [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 phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	78.2228	96	354	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	77.9878	108	354	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	77.9684	94	354	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	77.9471	95	354	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	77.9077	96	354	95	below_threshold
Bifidobacterium choerinum	strain=LMG 10510	GCA_000741135.1	35760	35760	type	True	77.8773	82	354	95	below_threshold
Bifidobacterium choloepi	strain=BRDM 6	GCA_010667615.1	2614131	2614131	type	True	77.8153	102	354	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	77.7348	114	354	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000771425.1	35760	35760	type	True	77.6538	91	354	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	77.6091	92	354	95	below_threshold
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	77.5537	87	354	95	below_threshold
Bifidobacterium cuniculi	strain=LMG 10738	GCA_000741575.1	1688	1688	type	True	77.5257	95	354	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	77.4507	97	354	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	77.4495	101	354	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	77.1002	50	354	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	77.0298	57	354	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	76.9456	53	354	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:16:02,977] [INFO] DFAST Taxonomy check result was written to GCA_017652165.1_ASM1765216v1_genomic.fna/tc_result.tsv
[2023-06-28 10:16:02,978] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:02,979] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:02,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/checkm_data
[2023-06-28 10:16:02,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:02,993] [INFO] Task started: CheckM
[2023-06-28 10:16:02,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017652165.1_ASM1765216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017652165.1_ASM1765216v1_genomic.fna/checkm_input GCA_017652165.1_ASM1765216v1_genomic.fna/checkm_result
[2023-06-28 10:16:18,554] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:18,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:18,574] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:18,574] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:18,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017652165.1_ASM1765216v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:18,575] [INFO] Task started: Blastn
[2023-06-28 10:16:18,575] [INFO] Running command: blastn -query GCA_017652165.1_ASM1765216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5959e85c-fd25-4a65-9879-796dad261af1/dqc_reference/reference_markers_gtdb.fasta -out GCA_017652165.1_ASM1765216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:20,220] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:20,223] [INFO] Selected 17 target genomes.
[2023-06-28 10:16:20,224] [INFO] Target genome list was writen to GCA_017652165.1_ASM1765216v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:20,239] [INFO] Task started: fastANI
[2023-06-28 10:16:20,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg5826f1d2-2fc2-4399-8971-d159d48e1711/GCA_017652165.1_ASM1765216v1_genomic.fna.gz --refList GCA_017652165.1_ASM1765216v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017652165.1_ASM1765216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:16:26,338] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:26,350] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:16:26,351] [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
GCA_017405305.1	s__RGIG7107 sp017405305	96.6042	340	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG7107	95.0	97.37	96.61	0.95	0.94	7	conclusive
GCA_017386585.1	s__RGIG7107 sp017386585	86.7345	271	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__RGIG7107	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	77.9878	108	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	77.9684	94	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000741135.1	s__Bifidobacterium choerinum	77.8381	83	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_010667615.1	s__Bifidobacterium choloepi	77.7825	103	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	77.7631	113	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234915.1	s__Galliscardovia vansinderenii	77.7609	84	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802875.1	s__Galliscardovia primatium	77.6114	89	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	77.5537	87	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903789535.1	s__Aeriscardovia sp903789535	77.5392	92	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Aeriscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741575.1	s__Bifidobacterium cuniculi	77.5257	95	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.4791	100	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	76.953	51	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	76.6715	64	354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
--------------------------------------------------------------------------------
[2023-06-28 10:16:26,352] [INFO] GTDB search result was written to GCA_017652165.1_ASM1765216v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:16:26,353] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:16:26,357] [INFO] DFAST_QC result json was written to GCA_017652165.1_ASM1765216v1_genomic.fna/dqc_result.json
[2023-06-28 10:16:26,357] [INFO] DFAST_QC completed!
[2023-06-28 10:16:26,357] [INFO] Total running time: 0h0m38s