[2024-01-24 11:12:39,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference
[2024-01-24 11:12:40,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,998] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,998] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfd1d4f1-a50f-43ee-a8e1-9a0e29b40db9/GCF_005405525.1_ASM540552v1_genomic.fna.gz | prodigal -d GCF_005405525.1_ASM540552v1_genomic.fna/cds.fna -a GCF_005405525.1_ASM540552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,739] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,740] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,740] [INFO] Running command: hmmsearch --tblout GCF_005405525.1_ASM540552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/reference_markers.hmm GCF_005405525.1_ASM540552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:48,018] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:48,019] [INFO] Found 6/6 markers.
[2024-01-24 11:12:48,047] [INFO] Query marker FASTA was written to GCF_005405525.1_ASM540552v1_genomic.fna/markers.fasta
[2024-01-24 11:12:48,047] [INFO] Task started: Blastn
[2024-01-24 11:12:48,048] [INFO] Running command: blastn -query GCF_005405525.1_ASM540552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/reference_markers.fasta -out GCF_005405525.1_ASM540552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,716] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,719] [INFO] Selected 16 target genomes.
[2024-01-24 11:12:48,719] [INFO] Target genome list was writen to GCF_005405525.1_ASM540552v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,762] [INFO] Task started: fastANI
[2024-01-24 11:12:48,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfd1d4f1-a50f-43ee-a8e1-9a0e29b40db9/GCF_005405525.1_ASM540552v1_genomic.fna.gz --refList GCF_005405525.1_ASM540552v1_genomic.fna/target_genomes.txt --output GCF_005405525.1_ASM540552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:54,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:54,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:54,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:54,031] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:54,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:54,031] [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 cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	100.0	759	760	95	conclusive
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	99.9602	738	760	95	conclusive
Weissella hellenica	strain=NBRC 15553	GCA_005405545.1	46256	46256	suspected-type	True	79.0971	121	760	95	below_threshold
Weissella paramesenteroides	strain=ATCC 33313	GCA_000160575.1	1249	1249	type	True	79.0024	120	760	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	78.8983	93	760	95	below_threshold
Weissella jogaejeotgali	strain=FOL01	GCA_001932615.1	1631871	1631871	type	True	78.8881	127	760	95	below_threshold
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	78.858	88	760	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	78.8557	116	760	95	below_threshold
Weissella viridescens	strain=NCTC13645	GCA_900460455.1	1629	1629	type	True	78.8443	102	760	95	below_threshold
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	78.8361	120	760	95	below_threshold
Weissella thailandensis	strain=KCTC 3751	GCA_003363255.1	89061	89061	type	True	78.5728	119	760	95	below_threshold
Weissella thailandensis	strain=JCM 10695	GCA_005405465.1	89061	89061	type	True	78.5579	123	760	95	below_threshold
Weissella bombi	strain=DSM 28794	GCA_005405505.1	1505725	1505725	type	True	78.4933	153	760	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	78.3946	152	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:54,033] [INFO] DFAST Taxonomy check result was written to GCF_005405525.1_ASM540552v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:54,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:54,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:54,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/checkm_data
[2024-01-24 11:12:54,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:54,060] [INFO] Task started: CheckM
[2024-01-24 11:12:54,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405525.1_ASM540552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405525.1_ASM540552v1_genomic.fna/checkm_input GCF_005405525.1_ASM540552v1_genomic.fna/checkm_result
[2024-01-24 11:13:20,975] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:20,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,995] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:20,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:20,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405525.1_ASM540552v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:20,996] [INFO] Task started: Blastn
[2024-01-24 11:13:20,996] [INFO] Running command: blastn -query GCF_005405525.1_ASM540552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7dcf76-9469-4c22-a3c1-c497086ef5d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405525.1_ASM540552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:22,009] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:22,013] [INFO] Selected 6 target genomes.
[2024-01-24 11:13:22,013] [INFO] Target genome list was writen to GCF_005405525.1_ASM540552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:22,019] [INFO] Task started: fastANI
[2024-01-24 11:13:22,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfd1d4f1-a50f-43ee-a8e1-9a0e29b40db9/GCF_005405525.1_ASM540552v1_genomic.fna.gz --refList GCF_005405525.1_ASM540552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405525.1_ASM540552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:25,463] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:25,469] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:25,469] [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_000193635.1	s__Weissella cibaria	99.9602	738	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	conclusive
GCF_004521965.1	s__Weissella cibaria_A	93.5542	575	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004766315.1	s__Weissella confusa_A	82.9589	379	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001436895.1	s__Weissella confusa	82.7876	390	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_004771295.1	s__Weissella confusa_B	82.5766	401	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:25,471] [INFO] GTDB search result was written to GCF_005405525.1_ASM540552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:25,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:25,476] [INFO] DFAST_QC result json was written to GCF_005405525.1_ASM540552v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:25,476] [INFO] DFAST_QC completed!
[2024-01-24 11:13:25,476] [INFO] Total running time: 0h0m46s