[2024-01-25 18:40:05,400] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference
[2024-01-25 18:40:06,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,563] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg80405d28-94e6-4d53-8ce3-70670d03d2d5/GCF_024701915.1_ASM2470191v1_genomic.fna.gz | prodigal -d GCF_024701915.1_ASM2470191v1_genomic.fna/cds.fna -a GCF_024701915.1_ASM2470191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:10,514] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:10,515] [INFO] Task started: HMMsearch
[2024-01-25 18:40:10,515] [INFO] Running command: hmmsearch --tblout GCF_024701915.1_ASM2470191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/reference_markers.hmm GCF_024701915.1_ASM2470191v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:10,697] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:10,698] [INFO] Found 6/6 markers.
[2024-01-25 18:40:10,716] [INFO] Query marker FASTA was written to GCF_024701915.1_ASM2470191v1_genomic.fna/markers.fasta
[2024-01-25 18:40:10,716] [INFO] Task started: Blastn
[2024-01-25 18:40:10,716] [INFO] Running command: blastn -query GCF_024701915.1_ASM2470191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/reference_markers.fasta -out GCF_024701915.1_ASM2470191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:11,263] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:11,268] [INFO] Selected 16 target genomes.
[2024-01-25 18:40:11,268] [INFO] Target genome list was writen to GCF_024701915.1_ASM2470191v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:11,274] [INFO] Task started: fastANI
[2024-01-25 18:40:11,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg80405d28-94e6-4d53-8ce3-70670d03d2d5/GCF_024701915.1_ASM2470191v1_genomic.fna.gz --refList GCF_024701915.1_ASM2470191v1_genomic.fna/target_genomes.txt --output GCF_024701915.1_ASM2470191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:18,496] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:18,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:18,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:18,507] [INFO] Found 15 fastANI hits (14 hits with ANI > threshold)
[2024-01-25 18:40:18,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:18,507] [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
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_001434635.1	29397	1584	suspected-type	True	98.5321	451	581	95	conclusive
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_000192165.1	29397	1584	suspected-type	True	98.3158	529	581	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001433875.1	83684	1584	suspected-type	True	98.1354	470	581	95	conclusive
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_002278095.1	29397	1584	type	True	98.1331	528	581	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_001437485.1	1537158	1584	suspected-type	True	98.0955	486	581	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=NBRC 3202	GCA_006740305.1	83684	1584	suspected-type	True	98.0152	527	581	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=ZN7a-9	GCA_000387565.1	1537158	1584	suspected-type	True	97.9553	491	581	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_004354615.1	1537158	1584	suspected-type	True	97.9142	502	581	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001908495.1	83684	1584	type	True	97.8876	510	581	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_001888925.1	1537158	1584	suspected-type	True	97.8241	519	581	95	conclusive
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001190005.1	1050107	1584	suspected-type	True	97.8096	529	581	95	conclusive
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001888965.1	1050107	1584	suspected-type	True	97.7978	535	581	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=NBRC 13953	GCA_006539405.1	1585	1584	type	True	97.342	466	581	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=ATCC 11842	GCA_000056065.1	1585	1584	type	True	97.1612	504	581	95	conclusive
Lactobacillus equicursoris	strain=JCM 14600	GCA_001311765.1	420645	420645	type	True	82.2196	375	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:18,509] [INFO] DFAST Taxonomy check result was written to GCF_024701915.1_ASM2470191v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:18,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:18,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:18,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/checkm_data
[2024-01-25 18:40:18,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:18,533] [INFO] Task started: CheckM
[2024-01-25 18:40:18,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024701915.1_ASM2470191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024701915.1_ASM2470191v1_genomic.fna/checkm_input GCF_024701915.1_ASM2470191v1_genomic.fna/checkm_result
[2024-01-25 18:40:36,438] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:36,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:36,454] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:36,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:36,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024701915.1_ASM2470191v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:36,455] [INFO] Task started: Blastn
[2024-01-25 18:40:36,455] [INFO] Running command: blastn -query GCF_024701915.1_ASM2470191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cf677d9-2c3d-4417-beb7-9fe2e5e97a5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024701915.1_ASM2470191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:37,231] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:37,234] [INFO] Selected 9 target genomes.
[2024-01-25 18:40:37,234] [INFO] Target genome list was writen to GCF_024701915.1_ASM2470191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:37,241] [INFO] Task started: fastANI
[2024-01-25 18:40:37,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg80405d28-94e6-4d53-8ce3-70670d03d2d5/GCF_024701915.1_ASM2470191v1_genomic.fna.gz --refList GCF_024701915.1_ASM2470191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024701915.1_ASM2470191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:40,719] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:40,724] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:40,724] [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_001433875.1	s__Lactobacillus delbrueckii	98.1354	470	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.56	96.59	0.89	0.81	103	conclusive
GCA_004556255.1	s__Lactobacillus delbrueckii_B	94.5277	349	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587775.1	s__Lactobacillus nasalidis	86.9435	345	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.92	99.91	0.92	0.89	3	-
GCF_009695985.1	s__Lactobacillus porci	82.5244	378	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.20	0.91	0.90	4	-
GCF_001434815.1	s__Lactobacillus equicursoris	82.4017	372	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.84	97.67	0.88	0.82	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:40,725] [INFO] GTDB search result was written to GCF_024701915.1_ASM2470191v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:40,726] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:40,728] [INFO] DFAST_QC result json was written to GCF_024701915.1_ASM2470191v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:40,729] [INFO] DFAST_QC completed!
[2024-01-25 18:40:40,729] [INFO] Total running time: 0h0m35s