[2024-01-24 13:22:13,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:13,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:13,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference
[2024-01-24 13:22:14,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:14,525] [INFO] Task started: Prodigal
[2024-01-24 13:22:14,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg495d7e7a-11f7-4509-bf08-101d3b80b9e3/GCF_009371885.1_ASM937188v1_genomic.fna.gz | prodigal -d GCF_009371885.1_ASM937188v1_genomic.fna/cds.fna -a GCF_009371885.1_ASM937188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:23,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:23,403] [INFO] Task started: HMMsearch
[2024-01-24 13:22:23,403] [INFO] Running command: hmmsearch --tblout GCF_009371885.1_ASM937188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/reference_markers.hmm GCF_009371885.1_ASM937188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:23,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:23,749] [INFO] Found 6/6 markers.
[2024-01-24 13:22:23,778] [INFO] Query marker FASTA was written to GCF_009371885.1_ASM937188v1_genomic.fna/markers.fasta
[2024-01-24 13:22:23,778] [INFO] Task started: Blastn
[2024-01-24 13:22:23,778] [INFO] Running command: blastn -query GCF_009371885.1_ASM937188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/reference_markers.fasta -out GCF_009371885.1_ASM937188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,769] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:24,769] [INFO] Target genome list was writen to GCF_009371885.1_ASM937188v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:24,784] [INFO] Task started: fastANI
[2024-01-24 13:22:24,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg495d7e7a-11f7-4509-bf08-101d3b80b9e3/GCF_009371885.1_ASM937188v1_genomic.fna.gz --refList GCF_009371885.1_ASM937188v1_genomic.fna/target_genomes.txt --output GCF_009371885.1_ASM937188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:33,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:33,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:33,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:33,274] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:33,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:33,275] [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 tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	100.0	898	900	95	conclusive
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	89.356	674	900	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	89.3446	682	900	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	89.3388	673	900	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	80.0011	304	900	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.7795	289	900	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	79.7171	297	900	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	79.7047	273	900	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=LMG 14934	GCA_000741375.1	78257	78448	type	True	79.5701	285	900	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	79.4549	280	900	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.3197	295	900	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.2775	70	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:33,277] [INFO] DFAST Taxonomy check result was written to GCF_009371885.1_ASM937188v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:33,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:33,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:33,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/checkm_data
[2024-01-24 13:22:33,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:33,326] [INFO] Task started: CheckM
[2024-01-24 13:22:33,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009371885.1_ASM937188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009371885.1_ASM937188v1_genomic.fna/checkm_input GCF_009371885.1_ASM937188v1_genomic.fna/checkm_result
[2024-01-24 13:23:06,047] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:06,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:06,074] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:06,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:06,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009371885.1_ASM937188v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:06,075] [INFO] Task started: Blastn
[2024-01-24 13:23:06,076] [INFO] Running command: blastn -query GCF_009371885.1_ASM937188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e67ad9a-1c6e-46e8-bed5-d9c1937a7356/dqc_reference/reference_markers_gtdb.fasta -out GCF_009371885.1_ASM937188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:07,410] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:07,414] [INFO] Selected 17 target genomes.
[2024-01-24 13:23:07,414] [INFO] Target genome list was writen to GCF_009371885.1_ASM937188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:07,438] [INFO] Task started: fastANI
[2024-01-24 13:23:07,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg495d7e7a-11f7-4509-bf08-101d3b80b9e3/GCF_009371885.1_ASM937188v1_genomic.fna.gz --refList GCF_009371885.1_ASM937188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009371885.1_ASM937188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:16,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:16,475] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:16,476] [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_009371885.1	s__Bifidobacterium tibiigranuli	100.0	899	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000741775.1	s__Bifidobacterium subtile	89.3446	682	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_001042635.1	s__Bifidobacterium scardovii	80.146	313	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	79.7785	279	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	79.7706	290	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.6462	284	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_012932365.1	s__Bifidobacterium sp012932365	79.5962	289	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.581	275	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	79.5761	275	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741285.1	s__Bifidobacterium mongoliense	79.5397	276	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	79.5208	311	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	79.5013	281	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_009299475.1	s__Bifidobacterium avesanii	79.4549	280	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741165.1	s__Bifidobacterium biavatii	79.4211	289	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.3014	285	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	79.2654	261	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_018555355.1	s__Bifidobacterium sp018555355	79.2231	291	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:16,477] [INFO] GTDB search result was written to GCF_009371885.1_ASM937188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:16,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:16,482] [INFO] DFAST_QC result json was written to GCF_009371885.1_ASM937188v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:16,482] [INFO] DFAST_QC completed!
[2024-01-24 13:23:16,482] [INFO] Total running time: 0h1m3s