[2024-01-25 17:43:35,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:35,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:35,640] [INFO] DQC Reference Directory: /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference
[2024-01-25 17:43:36,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:36,752] [INFO] Task started: Prodigal
[2024-01-25 17:43:36,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg8594d2ea-58fc-48a3-be44-446a60dba8e7/GCF_000770985.1_DSM-13734_genomic.fna.gz | prodigal -d GCF_000770985.1_DSM-13734_genomic.fna/cds.fna -a GCF_000770985.1_DSM-13734_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:45,168] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:45,168] [INFO] Task started: HMMsearch
[2024-01-25 17:43:45,168] [INFO] Running command: hmmsearch --tblout GCF_000770985.1_DSM-13734_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/reference_markers.hmm GCF_000770985.1_DSM-13734_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:45,377] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:45,378] [INFO] Found 6/6 markers.
[2024-01-25 17:43:45,408] [INFO] Query marker FASTA was written to GCF_000770985.1_DSM-13734_genomic.fna/markers.fasta
[2024-01-25 17:43:45,408] [INFO] Task started: Blastn
[2024-01-25 17:43:45,408] [INFO] Running command: blastn -query GCF_000770985.1_DSM-13734_genomic.fna/markers.fasta -db /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/reference_markers.fasta -out GCF_000770985.1_DSM-13734_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:46,472] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:46,475] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:46,475] [INFO] Target genome list was writen to GCF_000770985.1_DSM-13734_genomic.fna/target_genomes.txt
[2024-01-25 17:43:46,476] [INFO] Task started: fastANI
[2024-01-25 17:43:46,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg8594d2ea-58fc-48a3-be44-446a60dba8e7/GCF_000770985.1_DSM-13734_genomic.fna.gz --refList GCF_000770985.1_DSM-13734_genomic.fna/target_genomes.txt --output GCF_000770985.1_DSM-13734_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:55,493] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:55,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:55,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:55,503] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:43:55,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:55,503] [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=DSM 13734	GCA_000770985.1	158787	158787	type	True	100.0	992	996	95	conclusive
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	99.9982	990	996	95	conclusive
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	99.9888	988	996	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	84.1277	557	996	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	83.9582	573	996	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	83.9549	564	996	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	83.7979	567	996	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	83.6876	500	996	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	83.3529	483	996	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	82.9058	475	996	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.7105	483	996	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.866	324	996	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.3449	162	996	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.5311	136	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:55,504] [INFO] DFAST Taxonomy check result was written to GCF_000770985.1_DSM-13734_genomic.fna/tc_result.tsv
[2024-01-25 17:43:55,505] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:55,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:55,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/checkm_data
[2024-01-25 17:43:55,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:55,539] [INFO] Task started: CheckM
[2024-01-25 17:43:55,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000770985.1_DSM-13734_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000770985.1_DSM-13734_genomic.fna/checkm_input GCF_000770985.1_DSM-13734_genomic.fna/checkm_result
[2024-01-25 17:44:23,881] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:23,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:23,902] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:23,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:23,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000770985.1_DSM-13734_genomic.fna/markers.fasta)
[2024-01-25 17:44:23,903] [INFO] Task started: Blastn
[2024-01-25 17:44:23,904] [INFO] Running command: blastn -query GCF_000770985.1_DSM-13734_genomic.fna/markers.fasta -db /var/lib/cwl/stga194e402-7474-4e6c-8e19-347aa1c2f94d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000770985.1_DSM-13734_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:25,589] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:25,592] [INFO] Selected 16 target genomes.
[2024-01-25 17:44:25,592] [INFO] Target genome list was writen to GCF_000770985.1_DSM-13734_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:25,593] [INFO] Task started: fastANI
[2024-01-25 17:44:25,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg8594d2ea-58fc-48a3-be44-446a60dba8e7/GCF_000770985.1_DSM-13734_genomic.fna.gz --refList GCF_000770985.1_DSM-13734_genomic.fna/target_genomes_gtdb.txt --output GCF_000770985.1_DSM-13734_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:36,084] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:36,093] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:36,093] [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	99.9982	990	996	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	83.9456	565	996	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	83.7765	568	996	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	83.6533	501	996	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	83.5468	533	996	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	83.3904	481	996	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	83.3748	538	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	83.345	528	996	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	82.8699	477	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932365.1	s__Bifidobacterium sp012932365	82.7806	442	996	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	82.7224	469	996	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	82.6131	460	996	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	82.5923	464	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000771405.1	s__Bifidobacterium pullorum	82.2963	411	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	82.2875	414	996	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	82.0655	471	996	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:36,095] [INFO] GTDB search result was written to GCF_000770985.1_DSM-13734_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:36,095] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:36,098] [INFO] DFAST_QC result json was written to GCF_000770985.1_DSM-13734_genomic.fna/dqc_result.json
[2024-01-25 17:44:36,098] [INFO] DFAST_QC completed!
[2024-01-25 17:44:36,098] [INFO] Total running time: 0h1m0s