[2024-01-24 10:47:40,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference
[2024-01-24 10:47:44,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,786] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,787] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2e5c5e5-9701-4e58-a32b-2ff76b89cab7/GCF_010667655.1_ASM1066765v1_genomic.fna.gz | prodigal -d GCF_010667655.1_ASM1066765v1_genomic.fna/cds.fna -a GCF_010667655.1_ASM1066765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:53,593] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:53,593] [INFO] Task started: HMMsearch
[2024-01-24 10:47:53,593] [INFO] Running command: hmmsearch --tblout GCF_010667655.1_ASM1066765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/reference_markers.hmm GCF_010667655.1_ASM1066765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:53,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:53,853] [INFO] Found 6/6 markers.
[2024-01-24 10:47:53,875] [INFO] Query marker FASTA was written to GCF_010667655.1_ASM1066765v1_genomic.fna/markers.fasta
[2024-01-24 10:47:53,876] [INFO] Task started: Blastn
[2024-01-24 10:47:53,876] [INFO] Running command: blastn -query GCF_010667655.1_ASM1066765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/reference_markers.fasta -out GCF_010667655.1_ASM1066765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:54,891] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:54,896] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:54,897] [INFO] Target genome list was writen to GCF_010667655.1_ASM1066765v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:54,914] [INFO] Task started: fastANI
[2024-01-24 10:47:54,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e5c5e5-9701-4e58-a32b-2ff76b89cab7/GCF_010667655.1_ASM1066765v1_genomic.fna.gz --refList GCF_010667655.1_ASM1066765v1_genomic.fna/target_genomes.txt --output GCF_010667655.1_ASM1066765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:04,379] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:04,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:04,392] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:04,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:04,392] [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 saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	100.0	874	900	95	conclusive
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	94.8664	786	900	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	89.0888	700	900	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	86.5252	605	900	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	84.9442	565	900	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	84.5998	583	900	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	84.5548	586	900	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.4138	439	900	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	82.1763	411	900	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.7141	395	900	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.7111	421	900	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	81.3276	349	900	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.4557	110	900	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	76.2665	110	900	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	76.1913	115	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,394] [INFO] DFAST Taxonomy check result was written to GCF_010667655.1_ASM1066765v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:04,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:04,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:04,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/checkm_data
[2024-01-24 10:48:04,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:04,431] [INFO] Task started: CheckM
[2024-01-24 10:48:04,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010667655.1_ASM1066765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010667655.1_ASM1066765v1_genomic.fna/checkm_input GCF_010667655.1_ASM1066765v1_genomic.fna/checkm_result
[2024-01-24 10:48:34,943] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:34,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,964] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:34,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:34,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010667655.1_ASM1066765v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:34,965] [INFO] Task started: Blastn
[2024-01-24 10:48:34,965] [INFO] Running command: blastn -query GCF_010667655.1_ASM1066765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ac8bdb6-1e65-4c4d-b1b7-640e62dcc483/dqc_reference/reference_markers_gtdb.fasta -out GCF_010667655.1_ASM1066765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:36,429] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:36,433] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:36,433] [INFO] Target genome list was writen to GCF_010667655.1_ASM1066765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:36,443] [INFO] Task started: fastANI
[2024-01-24 10:48:36,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e5c5e5-9701-4e58-a32b-2ff76b89cab7/GCF_010667655.1_ASM1066765v1_genomic.fna.gz --refList GCF_010667655.1_ASM1066765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010667655.1_ASM1066765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:43,622] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:43,639] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:43,639] [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_010667655.1	s__Galliscardovia saimiriisciurei	100.0	872	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_002802875.1	s__Galliscardovia primatium	94.8664	786	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129925.1	s__Galliscardovia catulorum	86.5212	605	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	84.9592	564	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_002234915.1	s__Galliscardovia vansinderenii	84.5735	585	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	84.5621	586	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_002860365.1	s__Bifidobacterium parmae	82.4627	419	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_018555385.1	s__Bifidobacterium sp018555385	82.3618	442	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_018555635.1	s__Bifidobacterium sp018555635	82.0403	422	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_009193355.1	s__Bifidobacterium leontopitheci	81.9995	401	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_003952945.1	s__Bifidobacterium samirii	81.5643	372	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:43,641] [INFO] GTDB search result was written to GCF_010667655.1_ASM1066765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:43,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:43,644] [INFO] DFAST_QC result json was written to GCF_010667655.1_ASM1066765v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:43,644] [INFO] DFAST_QC completed!
[2024-01-24 10:48:43,644] [INFO] Total running time: 0h1m3s