[2024-01-24 12:21:59,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference
[2024-01-24 12:22:00,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,733] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,733] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9094776-5597-4d60-abb7-a8e102c3ca89/GCF_009078285.1_ASM907828v1_genomic.fna.gz | prodigal -d GCF_009078285.1_ASM907828v1_genomic.fna/cds.fna -a GCF_009078285.1_ASM907828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:09,890] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:09,891] [INFO] Task started: HMMsearch
[2024-01-24 12:22:09,891] [INFO] Running command: hmmsearch --tblout GCF_009078285.1_ASM907828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/reference_markers.hmm GCF_009078285.1_ASM907828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:10,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:10,166] [INFO] Found 6/6 markers.
[2024-01-24 12:22:10,193] [INFO] Query marker FASTA was written to GCF_009078285.1_ASM907828v1_genomic.fna/markers.fasta
[2024-01-24 12:22:10,193] [INFO] Task started: Blastn
[2024-01-24 12:22:10,194] [INFO] Running command: blastn -query GCF_009078285.1_ASM907828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/reference_markers.fasta -out GCF_009078285.1_ASM907828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:11,185] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:11,188] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:11,188] [INFO] Target genome list was writen to GCF_009078285.1_ASM907828v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:11,203] [INFO] Task started: fastANI
[2024-01-24 12:22:11,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9094776-5597-4d60-abb7-a8e102c3ca89/GCF_009078285.1_ASM907828v1_genomic.fna.gz --refList GCF_009078285.1_ASM907828v1_genomic.fna/target_genomes.txt --output GCF_009078285.1_ASM907828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:22,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:22,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:22,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:22,081] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:22,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:22,081] [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 jacchi	strain=MRM 9.3	GCA_009078285.1	2490545	2490545	type	True	99.9999	896	899	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.5609	447	899	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	82.4684	465	899	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	82.4539	459	899	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	82.4008	472	899	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	82.3627	454	899	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	82.2207	444	899	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	82.1777	415	899	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	82.1142	428	899	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	82.1136	434	899	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	81.6855	404	899	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.5273	411	899	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	81.0523	349	899	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_014898175.1	1603886	1603886	type	True	81.0192	362	899	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	80.9685	357	899	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.176	252	899	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	75.9865	78	899	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	75.9544	75	899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:22,083] [INFO] DFAST Taxonomy check result was written to GCF_009078285.1_ASM907828v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:22,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:22,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:22,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/checkm_data
[2024-01-24 12:22:22,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:22,115] [INFO] Task started: CheckM
[2024-01-24 12:22:22,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009078285.1_ASM907828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009078285.1_ASM907828v1_genomic.fna/checkm_input GCF_009078285.1_ASM907828v1_genomic.fna/checkm_result
[2024-01-24 12:22:55,409] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:55,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,435] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:55,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:55,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009078285.1_ASM907828v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:55,436] [INFO] Task started: Blastn
[2024-01-24 12:22:55,437] [INFO] Running command: blastn -query GCF_009078285.1_ASM907828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2dbfa37-dd4b-45cb-b132-2289e2799c69/dqc_reference/reference_markers_gtdb.fasta -out GCF_009078285.1_ASM907828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,945] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:56,945] [INFO] Target genome list was writen to GCF_009078285.1_ASM907828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:56,953] [INFO] Task started: fastANI
[2024-01-24 12:22:56,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9094776-5597-4d60-abb7-a8e102c3ca89/GCF_009078285.1_ASM907828v1_genomic.fna.gz --refList GCF_009078285.1_ASM907828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009078285.1_ASM907828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:04,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,993] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:04,993] [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_009078285.1	s__Bifidobacterium jacchi	99.9999	896	899	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_009299505.1	s__Bifidobacterium ramosum	82.4803	464	899	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	82.3733	453	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741175.1	s__Bifidobacterium callitrichos	82.3359	434	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_018555335.1	s__Bifidobacterium sp018555335	82.2715	446	899	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	82.1136	434	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000741165.1	s__Bifidobacterium biavatii	82.0828	447	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555635.1	s__Bifidobacterium sp018555635	81.8985	415	899	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	81.6855	404	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898155.1	s__Bifidobacterium eulemuris	81.0297	339	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	81.0106	361	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000741575.1	s__Bifidobacterium cuniculi	79.3565	270	899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,995] [INFO] GTDB search result was written to GCF_009078285.1_ASM907828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:04,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:05,000] [INFO] DFAST_QC result json was written to GCF_009078285.1_ASM907828v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:05,000] [INFO] DFAST_QC completed!
[2024-01-24 12:23:05,000] [INFO] Total running time: 0h1m6s