[2024-01-25 17:46:20,559] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference
[2024-01-25 17:46:21,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,723] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg546ef813-9236-4f41-a2e1-ed6226600ba7/GCF_024718545.1_ASM2471854v1_genomic.fna.gz | prodigal -d GCF_024718545.1_ASM2471854v1_genomic.fna/cds.fna -a GCF_024718545.1_ASM2471854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:25,322] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:25,322] [INFO] Task started: HMMsearch
[2024-01-25 17:46:25,322] [INFO] Running command: hmmsearch --tblout GCF_024718545.1_ASM2471854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/reference_markers.hmm GCF_024718545.1_ASM2471854v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:25,521] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:25,522] [INFO] Found 6/6 markers.
[2024-01-25 17:46:25,542] [INFO] Query marker FASTA was written to GCF_024718545.1_ASM2471854v1_genomic.fna/markers.fasta
[2024-01-25 17:46:25,543] [INFO] Task started: Blastn
[2024-01-25 17:46:25,543] [INFO] Running command: blastn -query GCF_024718545.1_ASM2471854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/reference_markers.fasta -out GCF_024718545.1_ASM2471854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:26,086] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:26,089] [INFO] Selected 11 target genomes.
[2024-01-25 17:46:26,089] [INFO] Target genome list was writen to GCF_024718545.1_ASM2471854v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:26,093] [INFO] Task started: fastANI
[2024-01-25 17:46:26,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg546ef813-9236-4f41-a2e1-ed6226600ba7/GCF_024718545.1_ASM2471854v1_genomic.fna.gz --refList GCF_024718545.1_ASM2471854v1_genomic.fna/target_genomes.txt --output GCF_024718545.1_ASM2471854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:30,568] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:30,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:30,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:30,574] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:30,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:30,575] [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
Weissella thailandensis	strain=JCM 10695	GCA_005405465.1	89061	89061	type	True	93.8942	532	611	95	below_threshold
Weissella jogaejeotgali	strain=FOL01	GCA_001932615.1	1631871	1631871	type	True	93.8436	542	611	95	below_threshold
Weissella thailandensis	strain=KCTC 3751	GCA_003363255.1	89061	89061	type	True	93.8352	525	611	95	below_threshold
Weissella thailandensis	strain=CCUG 46557	GCA_012396385.1	89061	89061	type	True	93.806	534	611	95	below_threshold
Weissella paramesenteroides	strain=ATCC 33313	GCA_000160575.1	1249	1249	type	True	83.8041	440	611	95	below_threshold
Weissella sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	81.3046	309	611	95	below_threshold
Periweissella fabaria	strain=LMG 24289 substr. LMG 24289	GCA_918814575.1	546157	546157	type	True	77.047	50	611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:30,577] [INFO] DFAST Taxonomy check result was written to GCF_024718545.1_ASM2471854v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:30,577] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:30,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:30,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/checkm_data
[2024-01-25 17:46:30,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:30,602] [INFO] Task started: CheckM
[2024-01-25 17:46:30,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024718545.1_ASM2471854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024718545.1_ASM2471854v1_genomic.fna/checkm_input GCF_024718545.1_ASM2471854v1_genomic.fna/checkm_result
[2024-01-25 17:46:47,699] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:47,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:47,719] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:47,719] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:47,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024718545.1_ASM2471854v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:47,720] [INFO] Task started: Blastn
[2024-01-25 17:46:47,720] [INFO] Running command: blastn -query GCF_024718545.1_ASM2471854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb21d757-0964-498c-96a9-12ee53731710/dqc_reference/reference_markers_gtdb.fasta -out GCF_024718545.1_ASM2471854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:48,461] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:48,468] [INFO] Selected 12 target genomes.
[2024-01-25 17:46:48,468] [INFO] Target genome list was writen to GCF_024718545.1_ASM2471854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:48,496] [INFO] Task started: fastANI
[2024-01-25 17:46:48,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg546ef813-9236-4f41-a2e1-ed6226600ba7/GCF_024718545.1_ASM2471854v1_genomic.fna.gz --refList GCF_024718545.1_ASM2471854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024718545.1_ASM2471854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:52,429] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:52,436] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:46:52,436] [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_005405465.1	s__Weissella thailandensis	93.8621	533	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_000160575.1	s__Weissella paramesenteroides	83.7562	442	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.27	97.99	0.88	0.85	25	-
GCF_006777025.1	s__Weissella hellenica_B	80.8121	316	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.22	98.80	0.93	0.90	9	-
GCF_005405545.1	s__Weissella hellenica	80.7016	328	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	99.99	0.99	0.99	4	-
GCF_900094835.1	s__Weissella bombi	80.1705	293	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004521965.1	s__Weissella cibaria_A	78.915	112	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437425.1	s__Weissella minor	78.7047	98	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
GCF_000420365.1	s__Weissella halotolerans	78.1405	67	611	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:52,437] [INFO] GTDB search result was written to GCF_024718545.1_ASM2471854v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:52,438] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:52,441] [INFO] DFAST_QC result json was written to GCF_024718545.1_ASM2471854v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:52,441] [INFO] DFAST_QC completed!
[2024-01-25 17:46:52,441] [INFO] Total running time: 0h0m32s