[2024-01-24 12:37:09,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference
[2024-01-24 12:37:11,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,124] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,124] [INFO] Running command: gunzip -c /var/lib/cwl/stge48b320c-85eb-4a20-981c-0016b3de9339/GCF_014635685.1_ASM1463568v1_genomic.fna.gz | prodigal -d GCF_014635685.1_ASM1463568v1_genomic.fna/cds.fna -a GCF_014635685.1_ASM1463568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:16,960] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:16,961] [INFO] Task started: HMMsearch
[2024-01-24 12:37:16,961] [INFO] Running command: hmmsearch --tblout GCF_014635685.1_ASM1463568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/reference_markers.hmm GCF_014635685.1_ASM1463568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:17,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:17,203] [INFO] Found 6/6 markers.
[2024-01-24 12:37:17,227] [INFO] Query marker FASTA was written to GCF_014635685.1_ASM1463568v1_genomic.fna/markers.fasta
[2024-01-24 12:37:17,228] [INFO] Task started: Blastn
[2024-01-24 12:37:17,228] [INFO] Running command: blastn -query GCF_014635685.1_ASM1463568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/reference_markers.fasta -out GCF_014635685.1_ASM1463568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:17,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:17,818] [INFO] Selected 21 target genomes.
[2024-01-24 12:37:17,819] [INFO] Target genome list was writen to GCF_014635685.1_ASM1463568v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:17,875] [INFO] Task started: fastANI
[2024-01-24 12:37:17,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge48b320c-85eb-4a20-981c-0016b3de9339/GCF_014635685.1_ASM1463568v1_genomic.fna.gz --refList GCF_014635685.1_ASM1463568v1_genomic.fna/target_genomes.txt --output GCF_014635685.1_ASM1463568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:24,349] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:24,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:24,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:24,356] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:24,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:24,356] [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
Galliscardovia ingluviei	strain=CCM 8606	GCA_014635685.1	1769422	1769422	type	True	100.0	689	689	95	conclusive
Gardnerella swidsinskii	strain=GS 9838-1	GCA_003397705.1	2792979	2792979	type	True	78.1715	54	689	95	below_threshold
Gardnerella leopoldii	strain=UGent 06.41	GCA_003293675.1	2792978	2792978	type	True	77.7975	55	689	95	below_threshold
Bifidobacterium tsurumiense	strain=DSM 17777	GCA_000771065.1	356829	356829	type	True	77.3217	59	689	95	below_threshold
Bifidobacterium tsurumiense	strain=DSM 17777	GCA_000429745.1	356829	356829	type	True	77.0587	58	689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:24,358] [INFO] DFAST Taxonomy check result was written to GCF_014635685.1_ASM1463568v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:24,359] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:24,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:24,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/checkm_data
[2024-01-24 12:37:24,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:24,388] [INFO] Task started: CheckM
[2024-01-24 12:37:24,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635685.1_ASM1463568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635685.1_ASM1463568v1_genomic.fna/checkm_input GCF_014635685.1_ASM1463568v1_genomic.fna/checkm_result
[2024-01-24 12:37:48,401] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:48,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:48,425] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:48,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:48,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635685.1_ASM1463568v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:48,426] [INFO] Task started: Blastn
[2024-01-24 12:37:48,426] [INFO] Running command: blastn -query GCF_014635685.1_ASM1463568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c082634-efa9-4812-938b-428dee244fc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635685.1_ASM1463568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:49,278] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:49,281] [INFO] Selected 24 target genomes.
[2024-01-24 12:37:49,282] [INFO] Target genome list was writen to GCF_014635685.1_ASM1463568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:49,361] [INFO] Task started: fastANI
[2024-01-24 12:37:49,361] [INFO] Running command: fastANI --query /var/lib/cwl/stge48b320c-85eb-4a20-981c-0016b3de9339/GCF_014635685.1_ASM1463568v1_genomic.fna.gz --refList GCF_014635685.1_ASM1463568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635685.1_ASM1463568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:56,573] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:56,589] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:56,589] [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_014635685.1	s__Galliscardovia ingluviei	100.0	689	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003397705.1	s__Bifidobacterium swidsinskii	78.1642	54	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.6629	98.35	97.96	0.94	0.90	18	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	78.1577	54	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	77.9676	60	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
GCA_003585735.1	s__Bifidobacterium sp003585735	77.9255	64	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
GCF_000263595.1	s__Bifidobacterium vaginale_E	77.8759	61	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.68	95.61	0.91	0.90	4	-
GCF_001546485.1	s__Bifidobacterium vaginale_D	77.8013	58	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.87	98.82	0.95	0.94	3	-
GCF_003408845.1	s__Bifidobacterium vaginale_H	77.7966	58	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293675.1	s__Bifidobacterium leopoldii	77.7561	57	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	98.89	98.40	0.95	0.92	16	-
GCF_000376885.1	s__Alloscardovia criceti	77.6522	53	689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:56,591] [INFO] GTDB search result was written to GCF_014635685.1_ASM1463568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:56,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:56,594] [INFO] DFAST_QC result json was written to GCF_014635685.1_ASM1463568v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:56,594] [INFO] DFAST_QC completed!
[2024-01-24 12:37:56,595] [INFO] Total running time: 0h0m47s