[2024-01-24 12:21:45,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:45,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:45,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference
[2024-01-24 12:21:46,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,376] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,376] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc5404a8-cbfc-4d23-bd86-5cac52fad901/GCF_000771545.1_DSM-21854_genomic.fna.gz | prodigal -d GCF_000771545.1_DSM-21854_genomic.fna/cds.fna -a GCF_000771545.1_DSM-21854_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:54,422] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:54,422] [INFO] Task started: HMMsearch
[2024-01-24 12:21:54,422] [INFO] Running command: hmmsearch --tblout GCF_000771545.1_DSM-21854_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/reference_markers.hmm GCF_000771545.1_DSM-21854_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:54,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:54,723] [INFO] Found 6/6 markers.
[2024-01-24 12:21:54,748] [INFO] Query marker FASTA was written to GCF_000771545.1_DSM-21854_genomic.fna/markers.fasta
[2024-01-24 12:21:54,748] [INFO] Task started: Blastn
[2024-01-24 12:21:54,749] [INFO] Running command: blastn -query GCF_000771545.1_DSM-21854_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/reference_markers.fasta -out GCF_000771545.1_DSM-21854_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:55,593] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:55,596] [INFO] Selected 13 target genomes.
[2024-01-24 12:21:55,596] [INFO] Target genome list was writen to GCF_000771545.1_DSM-21854_genomic.fna/target_genomes.txt
[2024-01-24 12:21:55,601] [INFO] Task started: fastANI
[2024-01-24 12:21:55,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc5404a8-cbfc-4d23-bd86-5cac52fad901/GCF_000771545.1_DSM-21854_genomic.fna.gz --refList GCF_000771545.1_DSM-21854_genomic.fna/target_genomes.txt --output GCF_000771545.1_DSM-21854_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:02,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:02,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:02,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:03,009] [INFO] Found 12 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:22:03,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:03,010] [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 catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000771545.1	630129	1686	type	True	100.0	752	753	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	99.9932	753	753	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	99.9694	736	753	95	conclusive
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	96.3644	565	753	95	conclusive
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	96.3486	543	753	95	conclusive
Bifidobacterium catenulatum	strain=JCM 1194	GCA_001025195.1	1686	1686	type	True	96.3332	577	753	95	conclusive
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000173435.1	28026	28026	type	True	92.4785	600	753	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	92.4614	598	753	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.9488	284	753	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.8513	290	753	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.783	284	753	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.461	91	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:03,018] [INFO] DFAST Taxonomy check result was written to GCF_000771545.1_DSM-21854_genomic.fna/tc_result.tsv
[2024-01-24 12:22:03,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:03,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:03,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/checkm_data
[2024-01-24 12:22:03,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:03,062] [INFO] Task started: CheckM
[2024-01-24 12:22:03,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771545.1_DSM-21854_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771545.1_DSM-21854_genomic.fna/checkm_input GCF_000771545.1_DSM-21854_genomic.fna/checkm_result
[2024-01-24 12:22:31,958] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:31,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:31,991] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:31,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:31,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771545.1_DSM-21854_genomic.fna/markers.fasta)
[2024-01-24 12:22:31,992] [INFO] Task started: Blastn
[2024-01-24 12:22:31,993] [INFO] Running command: blastn -query GCF_000771545.1_DSM-21854_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c6afa2-6058-416a-a80a-09d979f02d2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771545.1_DSM-21854_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:33,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:33,243] [INFO] Selected 5 target genomes.
[2024-01-24 12:22:33,244] [INFO] Target genome list was writen to GCF_000771545.1_DSM-21854_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:33,250] [INFO] Task started: fastANI
[2024-01-24 12:22:33,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc5404a8-cbfc-4d23-bd86-5cac52fad901/GCF_000771545.1_DSM-21854_genomic.fna.gz --refList GCF_000771545.1_DSM-21854_genomic.fna/target_genomes_gtdb.txt --output GCF_000771545.1_DSM-21854_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:36,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:36,386] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:36,387] [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_001042615.1	s__Bifidobacterium kashiwanohense	99.9932	753	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	conclusive
GCF_001025195.1	s__Bifidobacterium catenulatum	96.2954	578	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	95.0577	627	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_002742445.1	s__Bifidobacterium sp002742445	94.6106	596	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	92.4632	602	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:36,388] [INFO] GTDB search result was written to GCF_000771545.1_DSM-21854_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:36,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:36,392] [INFO] DFAST_QC result json was written to GCF_000771545.1_DSM-21854_genomic.fna/dqc_result.json
[2024-01-24 12:22:36,393] [INFO] DFAST_QC completed!
[2024-01-24 12:22:36,393] [INFO] Total running time: 0h0m51s