[2024-01-25 17:40:20,746] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference
[2024-01-25 17:40:21,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,840] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg142ad439-4a6b-4695-a6d7-00d88acab7e6/GCF_002259795.1_ASM225979v1_genomic.fna.gz | prodigal -d GCF_002259795.1_ASM225979v1_genomic.fna/cds.fna -a GCF_002259795.1_ASM225979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:29,498] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:29,498] [INFO] Task started: HMMsearch
[2024-01-25 17:40:29,498] [INFO] Running command: hmmsearch --tblout GCF_002259795.1_ASM225979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/reference_markers.hmm GCF_002259795.1_ASM225979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:29,704] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:29,705] [INFO] Found 6/6 markers.
[2024-01-25 17:40:29,725] [INFO] Query marker FASTA was written to GCF_002259795.1_ASM225979v1_genomic.fna/markers.fasta
[2024-01-25 17:40:29,726] [INFO] Task started: Blastn
[2024-01-25 17:40:29,726] [INFO] Running command: blastn -query GCF_002259795.1_ASM225979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/reference_markers.fasta -out GCF_002259795.1_ASM225979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:30,332] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:30,335] [INFO] Selected 17 target genomes.
[2024-01-25 17:40:30,336] [INFO] Target genome list was writen to GCF_002259795.1_ASM225979v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:30,357] [INFO] Task started: fastANI
[2024-01-25 17:40:30,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg142ad439-4a6b-4695-a6d7-00d88acab7e6/GCF_002259795.1_ASM225979v1_genomic.fna.gz --refList GCF_002259795.1_ASM225979v1_genomic.fna/target_genomes.txt --output GCF_002259795.1_ASM225979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:36,861] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:36,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:36,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:36,870] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:36,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:36,871] [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 aquikefiri	strain=LMG 28769	GCA_002259795.1	1653207	1653207	type	True	100.0	792	792	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	79.1531	127	792	95	below_threshold
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	79.0068	131	792	95	below_threshold
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	78.9674	129	792	95	below_threshold
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000741285.1	518643	518643	type	True	78.5868	65	792	95	below_threshold
Bifidobacterium crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	78.5437	117	792	95	below_threshold
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000771525.1	518643	518643	type	True	78.3855	63	792	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	78.0537	76	792	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	77.8949	78	792	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	77.2741	63	792	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	77.218	61	792	95	below_threshold
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	77.2027	60	792	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	76.8286	53	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:36,872] [INFO] DFAST Taxonomy check result was written to GCF_002259795.1_ASM225979v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:36,872] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:36,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:36,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/checkm_data
[2024-01-25 17:40:36,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:36,899] [INFO] Task started: CheckM
[2024-01-25 17:40:36,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259795.1_ASM225979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259795.1_ASM225979v1_genomic.fna/checkm_input GCF_002259795.1_ASM225979v1_genomic.fna/checkm_result
[2024-01-25 17:41:04,520] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:04,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:04,541] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:04,541] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:04,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259795.1_ASM225979v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:04,541] [INFO] Task started: Blastn
[2024-01-25 17:41:04,541] [INFO] Running command: blastn -query GCF_002259795.1_ASM225979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73aec7d4-ac57-42ec-b39e-1c11837ee70c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259795.1_ASM225979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:05,484] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:05,488] [INFO] Selected 19 target genomes.
[2024-01-25 17:41:05,488] [INFO] Target genome list was writen to GCF_002259795.1_ASM225979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:05,520] [INFO] Task started: fastANI
[2024-01-25 17:41:05,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg142ad439-4a6b-4695-a6d7-00d88acab7e6/GCF_002259795.1_ASM225979v1_genomic.fna.gz --refList GCF_002259795.1_ASM225979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259795.1_ASM225979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:14,739] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:14,748] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:14,748] [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_002259795.1	s__Bifidobacterium aquikefiri	100.0	792	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000741705.1	s__Bifidobacterium psychraerophilum	78.9674	129	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000741285.1	s__Bifidobacterium mongoliense	78.5868	65	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_000738005.1	s__Bifidobacterium crudilactis	78.5437	117	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	-
GCF_000741775.1	s__Bifidobacterium subtile	78.0537	76	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_002715865.1	s__Bifidobacterium asteroides	77.2741	63	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_009727065.1	s__Bifidobacterium canis	77.2267	50	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.79	99.79	0.97	0.97	2	-
GCF_009299485.1	s__Bifidobacterium apri	77.1595	61	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741695.1	s__Bifidobacterium reuteri	76.9564	61	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCA_002298605.1	s__Bifidobacterium sp002298605	76.8086	50	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.49	99.49	0.88	0.88	2	-
GCF_009193305.1	s__Bifidobacterium cebidarum	76.7923	60	792	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	76.7897	54	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_002802905.1	s__Galliscardovia simiarum	76.6511	54	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	76.5411	65	792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:14,749] [INFO] GTDB search result was written to GCF_002259795.1_ASM225979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:14,750] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:14,753] [INFO] DFAST_QC result json was written to GCF_002259795.1_ASM225979v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:14,753] [INFO] DFAST_QC completed!
[2024-01-25 17:41:14,753] [INFO] Total running time: 0h0m54s