[2024-01-25 17:42:50,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:50,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:50,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference
[2024-01-25 17:42:51,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:51,750] [INFO] Task started: Prodigal
[2024-01-25 17:42:51,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg120b351e-8ba0-4c21-8597-39c2709f5cb4/GCF_001042635.1_ASM104263v1_genomic.fna.gz | prodigal -d GCF_001042635.1_ASM104263v1_genomic.fna/cds.fna -a GCF_001042635.1_ASM104263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:00,942] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:00,943] [INFO] Task started: HMMsearch
[2024-01-25 17:43:00,943] [INFO] Running command: hmmsearch --tblout GCF_001042635.1_ASM104263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/reference_markers.hmm GCF_001042635.1_ASM104263v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:01,175] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:01,176] [INFO] Found 6/6 markers.
[2024-01-25 17:43:01,201] [INFO] Query marker FASTA was written to GCF_001042635.1_ASM104263v1_genomic.fna/markers.fasta
[2024-01-25 17:43:01,201] [INFO] Task started: Blastn
[2024-01-25 17:43:01,201] [INFO] Running command: blastn -query GCF_001042635.1_ASM104263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/reference_markers.fasta -out GCF_001042635.1_ASM104263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:02,280] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:02,282] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:02,283] [INFO] Target genome list was writen to GCF_001042635.1_ASM104263v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:02,285] [INFO] Task started: fastANI
[2024-01-25 17:43:02,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg120b351e-8ba0-4c21-8597-39c2709f5cb4/GCF_001042635.1_ASM104263v1_genomic.fna.gz --refList GCF_001042635.1_ASM104263v1_genomic.fna/target_genomes.txt --output GCF_001042635.1_ASM104263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:12,070] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:12,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:12,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:12,080] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:43:12,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:12,080] [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 scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	100.0	1050	1052	95	conclusive
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	99.9724	1024	1052	95	conclusive
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	99.9025	986	1052	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.9941	575	1052	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	83.9877	588	1052	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	83.9149	586	1052	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	83.8067	574	1052	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	83.6422	514	1052	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	83.5114	491	1052	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	83.036	484	1052	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.4474	507	1052	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.0518	328	1052	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.2918	177	1052	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.334	157	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:12,081] [INFO] DFAST Taxonomy check result was written to GCF_001042635.1_ASM104263v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:12,081] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:12,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:12,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/checkm_data
[2024-01-25 17:43:12,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:12,114] [INFO] Task started: CheckM
[2024-01-25 17:43:12,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042635.1_ASM104263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042635.1_ASM104263v1_genomic.fna/checkm_input GCF_001042635.1_ASM104263v1_genomic.fna/checkm_result
[2024-01-25 17:43:43,869] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:43,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:43,893] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:43,893] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:43,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042635.1_ASM104263v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:43,894] [INFO] Task started: Blastn
[2024-01-25 17:43:43,894] [INFO] Running command: blastn -query GCF_001042635.1_ASM104263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e25a7c-770d-43b2-879b-56e19f3fb11d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042635.1_ASM104263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:45,613] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:45,615] [INFO] Selected 16 target genomes.
[2024-01-25 17:43:45,616] [INFO] Target genome list was writen to GCF_001042635.1_ASM104263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:45,622] [INFO] Task started: fastANI
[2024-01-25 17:43:45,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg120b351e-8ba0-4c21-8597-39c2709f5cb4/GCF_001042635.1_ASM104263v1_genomic.fna.gz --refList GCF_001042635.1_ASM104263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001042635.1_ASM104263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:55,893] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:55,903] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:55,903] [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_001042635.1	s__Bifidobacterium scardovii	100.0	1051	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	conclusive
GCF_009299505.1	s__Bifidobacterium ramosum	83.9645	583	1052	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	83.7621	577	1052	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	83.7283	542	1052	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	83.6695	512	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	83.5114	491	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	83.3983	542	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	83.3385	551	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	83.0804	483	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	82.785	474	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	82.6909	473	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012932365.1	s__Bifidobacterium sp012932365	82.6567	451	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	82.6263	472	1052	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	82.2273	426	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_014898175.1	s__Bifidobacterium lemurum	82.217	478	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000771405.1	s__Bifidobacterium pullorum	82.0562	425	1052	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:55,905] [INFO] GTDB search result was written to GCF_001042635.1_ASM104263v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:55,905] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:55,910] [INFO] DFAST_QC result json was written to GCF_001042635.1_ASM104263v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:55,910] [INFO] DFAST_QC completed!
[2024-01-25 17:43:55,911] [INFO] Total running time: 0h1m5s