[2024-01-24 14:10:13,737] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:13,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:13,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference
[2024-01-24 14:10:14,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:14,910] [INFO] Task started: Prodigal
[2024-01-24 14:10:14,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgb935503d-317d-44fe-8bad-3b7282125bca/GCF_000771485.1_DSM-20456_genomic.fna.gz | prodigal -d GCF_000771485.1_DSM-20456_genomic.fna/cds.fna -a GCF_000771485.1_DSM-20456_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:21,841] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:21,842] [INFO] Task started: HMMsearch
[2024-01-24 14:10:21,842] [INFO] Running command: hmmsearch --tblout GCF_000771485.1_DSM-20456_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/reference_markers.hmm GCF_000771485.1_DSM-20456_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:22,015] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:22,016] [INFO] Found 6/6 markers.
[2024-01-24 14:10:22,037] [INFO] Query marker FASTA was written to GCF_000771485.1_DSM-20456_genomic.fna/markers.fasta
[2024-01-24 14:10:22,037] [INFO] Task started: Blastn
[2024-01-24 14:10:22,037] [INFO] Running command: blastn -query GCF_000771485.1_DSM-20456_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/reference_markers.fasta -out GCF_000771485.1_DSM-20456_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:22,888] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:22,891] [INFO] Selected 10 target genomes.
[2024-01-24 14:10:22,892] [INFO] Target genome list was writen to GCF_000771485.1_DSM-20456_genomic.fna/target_genomes.txt
[2024-01-24 14:10:22,913] [INFO] Task started: fastANI
[2024-01-24 14:10:22,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgb935503d-317d-44fe-8bad-3b7282125bca/GCF_000771485.1_DSM-20456_genomic.fna.gz --refList GCF_000771485.1_DSM-20456_genomic.fna/target_genomes.txt --output GCF_000771485.1_DSM-20456_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:27,941] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:27,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:27,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:27,951] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:10:27,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:10:27,951] [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 bifidum	strain=DSM 20456	GCA_000771485.1	1681	1681	type	True	100.0	711	713	95	conclusive
Bifidobacterium bifidum	strain=JCM 1255	GCA_001025135.1	1681	1681	type	True	99.9996	712	713	95	conclusive
Bifidobacterium bifidum	strain=NCTC13001	GCA_900637095.1	1681	1681	type	True	99.9989	713	713	95	conclusive
Bifidobacterium bifidum	strain=LMG 11041	GCA_000741085.1	1681	1681	type	True	99.9929	713	713	95	conclusive
Bifidobacterium bifidum	strain=ATCC 29521	GCA_000466525.1	1681	1681	type	True	99.9805	704	713	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.6102	406	713	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.0133	377	713	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.633	251	713	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.4968	133	713	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.0606	77	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:27,953] [INFO] DFAST Taxonomy check result was written to GCF_000771485.1_DSM-20456_genomic.fna/tc_result.tsv
[2024-01-24 14:10:27,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:27,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:27,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/checkm_data
[2024-01-24 14:10:27,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:27,978] [INFO] Task started: CheckM
[2024-01-24 14:10:27,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771485.1_DSM-20456_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771485.1_DSM-20456_genomic.fna/checkm_input GCF_000771485.1_DSM-20456_genomic.fna/checkm_result
[2024-01-24 14:10:53,034] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:53,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:53,051] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:53,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:53,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771485.1_DSM-20456_genomic.fna/markers.fasta)
[2024-01-24 14:10:53,052] [INFO] Task started: Blastn
[2024-01-24 14:10:53,052] [INFO] Running command: blastn -query GCF_000771485.1_DSM-20456_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d6501f-1d04-4abd-817d-6fa835f59533/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771485.1_DSM-20456_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:54,261] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:54,264] [INFO] Selected 18 target genomes.
[2024-01-24 14:10:54,264] [INFO] Target genome list was writen to GCF_000771485.1_DSM-20456_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:54,332] [INFO] Task started: fastANI
[2024-01-24 14:10:54,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgb935503d-317d-44fe-8bad-3b7282125bca/GCF_000771485.1_DSM-20456_genomic.fna.gz --refList GCF_000771485.1_DSM-20456_genomic.fna/target_genomes_gtdb.txt --output GCF_000771485.1_DSM-20456_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:03,409] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:03,423] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:03,423] [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_001025135.1	s__Bifidobacterium bifidum	99.9996	712	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	conclusive
GCF_009193355.1	s__Bifidobacterium leontopitheci	83.4847	491	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.6175	441	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_010667685.1	s__Bifidobacterium aerophilum	82.4701	424	713	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	82.456	397	713	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	82.3754	386	713	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	82.3305	398	713	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	82.2983	402	713	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	82.2511	404	713	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	82.1834	399	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	82.0888	435	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	82.0271	385	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196555.1	s__Bifidobacterium longum	82.0127	349	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_000269965.1	s__Bifidobacterium infantis	81.8723	362	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_009078285.1	s__Bifidobacterium jacchi	81.6968	400	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771405.1	s__Bifidobacterium pullorum	81.5329	321	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003951095.1	s__Bifidobacterium goeldii	80.767	283	713	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 14:11:03,424] [INFO] GTDB search result was written to GCF_000771485.1_DSM-20456_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:03,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:03,428] [INFO] DFAST_QC result json was written to GCF_000771485.1_DSM-20456_genomic.fna/dqc_result.json
[2024-01-24 14:11:03,428] [INFO] DFAST_QC completed!
[2024-01-24 14:11:03,428] [INFO] Total running time: 0h0m50s