[2024-01-24 13:46:55,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:55,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:55,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference
[2024-01-24 13:46:56,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:56,800] [INFO] Task started: Prodigal
[2024-01-24 13:46:56,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d2859ce-1798-496c-ab0a-404b48e0c4e6/GCF_000191785.1_ASM19178v1_genomic.fna.gz | prodigal -d GCF_000191785.1_ASM19178v1_genomic.fna/cds.fna -a GCF_000191785.1_ASM19178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:02,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:02,655] [INFO] Task started: HMMsearch
[2024-01-24 13:47:02,655] [INFO] Running command: hmmsearch --tblout GCF_000191785.1_ASM19178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/reference_markers.hmm GCF_000191785.1_ASM19178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:02,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:02,866] [INFO] Found 6/6 markers.
[2024-01-24 13:47:02,895] [INFO] Query marker FASTA was written to GCF_000191785.1_ASM19178v1_genomic.fna/markers.fasta
[2024-01-24 13:47:02,896] [INFO] Task started: Blastn
[2024-01-24 13:47:02,896] [INFO] Running command: blastn -query GCF_000191785.1_ASM19178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/reference_markers.fasta -out GCF_000191785.1_ASM19178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:03,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:03,713] [INFO] Selected 21 target genomes.
[2024-01-24 13:47:03,713] [INFO] Target genome list was writen to GCF_000191785.1_ASM19178v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:03,740] [INFO] Task started: fastANI
[2024-01-24 13:47:03,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2859ce-1798-496c-ab0a-404b48e0c4e6/GCF_000191785.1_ASM19178v1_genomic.fna.gz --refList GCF_000191785.1_ASM19178v1_genomic.fna/target_genomes.txt --output GCF_000191785.1_ASM19178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:14,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:14,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:14,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:14,821] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:14,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:14,821] [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
Parascardovia denticolens	strain=DSM 10105	GCA_000191785.1	78258	78258	type	True	100.0	630	630	95	conclusive
Parascardovia denticolens	strain=JCM 12538	GCA_001042675.1	78258	78258	type	True	99.9997	628	630	95	conclusive
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	78.345	86	630	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_014898175.1	1603886	1603886	type	True	77.9678	106	630	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.9592	113	630	95	below_threshold
Pseudoscardovia radai	strain=DSM 24742	GCA_002259605.1	987066	987066	type	True	77.9239	89	630	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.8873	115	630	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	77.8791	116	630	95	below_threshold
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	77.8691	96	630	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	77.8524	124	630	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	77.7606	100	630	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	77.7335	112	630	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	77.6882	101	630	95	below_threshold
Bifidobacterium moukalabense	strain=GG01	GCA_005405645.1	1333651	1333651	type	True	77.475	101	630	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	77.4635	93	630	95	below_threshold
Pseudoscardovia suis	strain=DSM 24744	GCA_002259715.1	987063	987063	type	True	77.419	78	630	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	77.337	95	630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,834] [INFO] DFAST Taxonomy check result was written to GCF_000191785.1_ASM19178v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:14,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:14,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:14,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/checkm_data
[2024-01-24 13:47:14,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:14,862] [INFO] Task started: CheckM
[2024-01-24 13:47:14,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000191785.1_ASM19178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000191785.1_ASM19178v1_genomic.fna/checkm_input GCF_000191785.1_ASM19178v1_genomic.fna/checkm_result
[2024-01-24 13:47:37,686] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:37,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,705] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:37,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:37,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000191785.1_ASM19178v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:37,706] [INFO] Task started: Blastn
[2024-01-24 13:47:37,707] [INFO] Running command: blastn -query GCF_000191785.1_ASM19178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92001186-ccca-41f4-baba-d736a7c68fb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000191785.1_ASM19178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:38,896] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:38,900] [INFO] Selected 23 target genomes.
[2024-01-24 13:47:38,901] [INFO] Target genome list was writen to GCF_000191785.1_ASM19178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:38,925] [INFO] Task started: fastANI
[2024-01-24 13:47:38,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2859ce-1798-496c-ab0a-404b48e0c4e6/GCF_000191785.1_ASM19178v1_genomic.fna.gz --refList GCF_000191785.1_ASM19178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000191785.1_ASM19178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:48,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:48,024] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:48,025] [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_001042675.1	s__Parascardovia denticolens	99.9997	629	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Parascardovia	95.0	99.43	98.73	0.96	0.91	5	conclusive
GCF_003202755.1	s__Bifidobacterium asteroides_F	78.3924	98	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042595.1	s__Bifidobacterium dentium	78.345	86	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	78.2656	111	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_000010425.1	s__Bifidobacterium adolescentis	78.1951	105	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	78.1791	120	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_016100725.1	s__Bifidobacterium sp016100725	78.1172	117	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	78.1148	107	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002715865.1	s__Bifidobacterium asteroides	78.0603	117	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_000499185.1	s__Bifidobacterium sp000499185	77.9212	116	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	-
GCF_000522505.1	s__Bifidobacterium moukalabense	77.9194	98	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_003202715.1	s__Bifidobacterium asteroides_E	77.8362	96	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	-
GCF_014898175.1	s__Bifidobacterium lemurum	77.8316	105	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002802875.1	s__Galliscardovia primatium	77.8103	99	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.8073	96	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.8021	91	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_003129925.1	s__Galliscardovia catulorum	77.7737	88	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000269605.1	s__Scardovia wiggsiae	77.6389	60	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Scardovia	95.0	97.70	96.37	0.97	0.95	5	-
GCA_002353815.1	s__Pseudoscardovia sp002353815	77.364	91	630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:48,026] [INFO] GTDB search result was written to GCF_000191785.1_ASM19178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:48,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:48,031] [INFO] DFAST_QC result json was written to GCF_000191785.1_ASM19178v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:48,032] [INFO] DFAST_QC completed!
[2024-01-24 13:47:48,032] [INFO] Total running time: 0h0m53s