[2024-01-25 19:49:50,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:50,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:50,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference
[2024-01-25 19:49:51,983] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:51,984] [INFO] Task started: Prodigal
[2024-01-25 19:49:51,984] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa5b35c4-8939-47c6-9979-d885a345768d/GCF_009299475.1_ASM929947v1_genomic.fna.gz | prodigal -d GCF_009299475.1_ASM929947v1_genomic.fna/cds.fna -a GCF_009299475.1_ASM929947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:59,635] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:59,635] [INFO] Task started: HMMsearch
[2024-01-25 19:49:59,635] [INFO] Running command: hmmsearch --tblout GCF_009299475.1_ASM929947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/reference_markers.hmm GCF_009299475.1_ASM929947v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:59,821] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:59,822] [INFO] Found 6/6 markers.
[2024-01-25 19:49:59,846] [INFO] Query marker FASTA was written to GCF_009299475.1_ASM929947v1_genomic.fna/markers.fasta
[2024-01-25 19:49:59,846] [INFO] Task started: Blastn
[2024-01-25 19:49:59,846] [INFO] Running command: blastn -query GCF_009299475.1_ASM929947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/reference_markers.fasta -out GCF_009299475.1_ASM929947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:00,955] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:00,958] [INFO] Selected 18 target genomes.
[2024-01-25 19:50:00,958] [INFO] Target genome list was writen to GCF_009299475.1_ASM929947v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:00,963] [INFO] Task started: fastANI
[2024-01-25 19:50:00,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5b35c4-8939-47c6-9979-d885a345768d/GCF_009299475.1_ASM929947v1_genomic.fna.gz --refList GCF_009299475.1_ASM929947v1_genomic.fna/target_genomes.txt --output GCF_009299475.1_ASM929947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:11,409] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:11,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:11,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:11,421] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:50:11,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:11,421] [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 avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	100.0	865	867	95	conclusive
Bifidobacterium avesanii	strain=TREC	GCA_010667745.1	1798157	1798157	type	True	99.9891	852	867	95	conclusive
Bifidobacterium vespertilionis	strain=RST16	GCA_008698145.1	2562524	2562524	type	True	86.9235	613	867	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	83.899	490	867	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	83.7164	467	867	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	83.5588	456	867	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	83.4479	457	867	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	83.3726	469	867	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.2379	483	867	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.0803	477	867	95	below_threshold
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	82.9903	457	867	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	82.8864	457	867	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	82.7645	460	867	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	82.6616	472	867	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	81.6661	355	867	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.9417	306	867	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.6021	174	867	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.701	169	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:11,423] [INFO] DFAST Taxonomy check result was written to GCF_009299475.1_ASM929947v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:11,423] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:11,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:11,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/checkm_data
[2024-01-25 19:50:11,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:11,453] [INFO] Task started: CheckM
[2024-01-25 19:50:11,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299475.1_ASM929947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299475.1_ASM929947v1_genomic.fna/checkm_input GCF_009299475.1_ASM929947v1_genomic.fna/checkm_result
[2024-01-25 19:50:40,381] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:40,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:40,402] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:40,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:40,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299475.1_ASM929947v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:40,403] [INFO] Task started: Blastn
[2024-01-25 19:50:40,403] [INFO] Running command: blastn -query GCF_009299475.1_ASM929947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d0eacff-04af-4d60-96fc-9664b1e5e0d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299475.1_ASM929947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:42,170] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:42,173] [INFO] Selected 13 target genomes.
[2024-01-25 19:50:42,173] [INFO] Target genome list was writen to GCF_009299475.1_ASM929947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:42,184] [INFO] Task started: fastANI
[2024-01-25 19:50:42,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa5b35c4-8939-47c6-9979-d885a345768d/GCF_009299475.1_ASM929947v1_genomic.fna.gz --refList GCF_009299475.1_ASM929947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299475.1_ASM929947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:50,806] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:50,815] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:50,816] [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_009299475.1	s__Bifidobacterium avesanii	100.0	865	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_012932365.1	s__Bifidobacterium sp012932365	87.1847	607	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698145.1	s__Bifidobacterium vespertilionis	86.8956	615	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	-
GCF_018555385.1	s__Bifidobacterium sp018555385	83.8752	491	867	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	83.6779	469	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	83.5388	457	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	83.3948	460	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	83.3397	471	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	82.9762	458	867	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	82.8725	457	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.6506	480	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003129925.1	s__Galliscardovia catulorum	81.6937	353	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298605.1	s__Bifidobacterium sp002298605	81.467	344	867	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.49	99.49	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:50,817] [INFO] GTDB search result was written to GCF_009299475.1_ASM929947v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:50,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:50,824] [INFO] DFAST_QC result json was written to GCF_009299475.1_ASM929947v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:50,825] [INFO] DFAST_QC completed!
[2024-01-25 19:50:50,825] [INFO] Total running time: 0h1m0s