[2024-01-24 10:47:10,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,260] [INFO] DQC Reference Directory: /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference
[2024-01-24 10:47:12,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,199] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,200] [INFO] Running command: gunzip -c /var/lib/cwl/stged70ae77-db0f-4000-ac3d-ed414a5744fc/GCF_003293675.1_ASM329367v1_genomic.fna.gz | prodigal -d GCF_003293675.1_ASM329367v1_genomic.fna/cds.fna -a GCF_003293675.1_ASM329367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:16,134] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:16,134] [INFO] Task started: HMMsearch
[2024-01-24 10:47:16,134] [INFO] Running command: hmmsearch --tblout GCF_003293675.1_ASM329367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/reference_markers.hmm GCF_003293675.1_ASM329367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:16,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:16,491] [INFO] Found 6/6 markers.
[2024-01-24 10:47:16,509] [INFO] Query marker FASTA was written to GCF_003293675.1_ASM329367v1_genomic.fna/markers.fasta
[2024-01-24 10:47:16,533] [INFO] Task started: Blastn
[2024-01-24 10:47:16,533] [INFO] Running command: blastn -query GCF_003293675.1_ASM329367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/reference_markers.fasta -out GCF_003293675.1_ASM329367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,576] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,581] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:19,581] [INFO] Target genome list was writen to GCF_003293675.1_ASM329367v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,562] [INFO] Task started: fastANI
[2024-01-24 10:47:22,563] [INFO] Running command: fastANI --query /var/lib/cwl/stged70ae77-db0f-4000-ac3d-ed414a5744fc/GCF_003293675.1_ASM329367v1_genomic.fna.gz --refList GCF_003293675.1_ASM329367v1_genomic.fna/target_genomes.txt --output GCF_003293675.1_ASM329367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:27,839] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:27,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:27,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:27,850] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:27,850] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:27,850] [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
Gardnerella leopoldii	strain=UGent 06.41	GCA_003293675.1	2792978	2792978	type	True	100.0	521	521	95	inconclusive
Gardnerella swidsinskii	strain=GS 9838-1	GCA_003397705.1	2792979	2792979	type	True	95.6629	458	521	95	inconclusive
Gardnerella vaginalis	strain=JCM 11026	GCA_001042655.1	2702	2702	suspected-type	True	83.8714	282	521	95	below_threshold
Gardnerella vaginalis	strain=DSM 4944	GCA_900105405.1	2702	2702	suspected-type	True	83.7526	279	521	95	below_threshold
Gardnerella vaginalis	strain=ATCC 14018	GCA_003397685.1	2702	2702	suspected-type	True	83.6655	284	521	95	below_threshold
Gardnerella vaginalis	strain=ATCC 14018	GCA_000178355.1	2702	2702	suspected-type	True	83.2787	246	521	95	below_threshold
Gardnerella piotii	strain=UGent 18.01	GCA_003397585.1	2792977	2792977	type	True	82.7427	277	521	95	below_threshold
Galliscardovia ingluviei	strain=CCM 8606	GCA_014635685.1	1769422	1769422	type	True	77.7414	50	521	95	below_threshold
Alloscardovia omnicolens	strain=DSM 21503	GCA_000420505.1	419015	419015	type	True	77.4851	53	521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:27,852] [INFO] DFAST Taxonomy check result was written to GCF_003293675.1_ASM329367v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:27,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:27,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:27,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/checkm_data
[2024-01-24 10:47:27,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:27,875] [INFO] Task started: CheckM
[2024-01-24 10:47:27,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003293675.1_ASM329367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003293675.1_ASM329367v1_genomic.fna/checkm_input GCF_003293675.1_ASM329367v1_genomic.fna/checkm_result
[2024-01-24 10:47:48,157] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:48,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:48,176] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:48,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:48,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003293675.1_ASM329367v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:48,182] [INFO] Task started: Blastn
[2024-01-24 10:47:48,183] [INFO] Running command: blastn -query GCF_003293675.1_ASM329367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge72791c6-89c6-4167-9007-bea72ad46013/dqc_reference/reference_markers_gtdb.fasta -out GCF_003293675.1_ASM329367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:49,484] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:49,487] [INFO] Selected 9 target genomes.
[2024-01-24 10:47:49,487] [INFO] Target genome list was writen to GCF_003293675.1_ASM329367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:50,765] [INFO] Task started: fastANI
[2024-01-24 10:47:50,766] [INFO] Running command: fastANI --query /var/lib/cwl/stged70ae77-db0f-4000-ac3d-ed414a5744fc/GCF_003293675.1_ASM329367v1_genomic.fna.gz --refList GCF_003293675.1_ASM329367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003293675.1_ASM329367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:47:54,887] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:54,901] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:47:54,902] [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_003293675.1	s__Bifidobacterium leopoldii	100.0	521	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	98.89	98.40	0.95	0.92	16	conclusive
GCA_003585845.1	s__Bifidobacterium sp003585845	95.706	472	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	N/A	N/A	N/A	N/A	1	conclusive
GCF_003397705.1	s__Bifidobacterium swidsinskii	95.6629	458	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.6629	98.35	97.96	0.94	0.90	18	conclusive
GCF_000263595.1	s__Bifidobacterium vaginale_E	87.0964	403	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.68	95.61	0.91	0.90	4	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	86.5662	399	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	86.3619	336	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003585735.1	s__Bifidobacterium sp003585735	86.0303	395	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
GCF_003408845.1	s__Bifidobacterium vaginale_H	85.0818	388	521	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 10:47:54,903] [INFO] GTDB search result was written to GCF_003293675.1_ASM329367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:47:54,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:47:54,909] [INFO] DFAST_QC result json was written to GCF_003293675.1_ASM329367v1_genomic.fna/dqc_result.json
[2024-01-24 10:47:54,909] [INFO] DFAST_QC completed!
[2024-01-24 10:47:54,909] [INFO] Total running time: 0h0m45s