[2024-01-24 13:09:51,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference
[2024-01-24 13:09:53,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,071] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,071] [INFO] Running command: gunzip -c /var/lib/cwl/stgff9fee93-df60-4c99-8b97-1d475eefaaa5/GCF_000277645.1_ASM27764v1_genomic.fna.gz | prodigal -d GCF_000277645.1_ASM27764v1_genomic.fna/cds.fna -a GCF_000277645.1_ASM27764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:56,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:56,517] [INFO] Task started: HMMsearch
[2024-01-24 13:09:56,518] [INFO] Running command: hmmsearch --tblout GCF_000277645.1_ASM27764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/reference_markers.hmm GCF_000277645.1_ASM27764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:56,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:56,777] [INFO] Found 6/6 markers.
[2024-01-24 13:09:56,799] [INFO] Query marker FASTA was written to GCF_000277645.1_ASM27764v1_genomic.fna/markers.fasta
[2024-01-24 13:09:56,800] [INFO] Task started: Blastn
[2024-01-24 13:09:56,800] [INFO] Running command: blastn -query GCF_000277645.1_ASM27764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/reference_markers.fasta -out GCF_000277645.1_ASM27764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:57,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:57,416] [INFO] Selected 20 target genomes.
[2024-01-24 13:09:57,417] [INFO] Target genome list was writen to GCF_000277645.1_ASM27764v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:57,424] [INFO] Task started: fastANI
[2024-01-24 13:09:57,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgff9fee93-df60-4c99-8b97-1d475eefaaa5/GCF_000277645.1_ASM27764v1_genomic.fna.gz --refList GCF_000277645.1_ASM27764v1_genomic.fna/target_genomes.txt --output GCF_000277645.1_ASM27764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:03,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:03,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:03,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:03,958] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:03,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:03,958] [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 koreensis	strain=KCTC 3621	GCA_000277645.1	165096	165096	type	True	100.0	532	568	95	conclusive
Weissella coleopterorum	strain=HDW19	GCA_011304355.1	2714949	2714949	type	True	81.9577	317	568	95	below_threshold
Weissella diestrammenae	strain=KACC 16890	GCA_014397255.1	1162633	1162633	type	True	80.0516	109	568	95	below_threshold
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	79.7184	58	568	95	below_threshold
Weissella sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	78.9625	76	568	95	below_threshold
Weissella kandleri	strain=DSM 20593	GCA_001438705.1	1616	1616	type	True	78.8064	135	568	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	78.7137	57	568	95	below_threshold
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	78.5675	63	568	95	below_threshold
Weissella paramesenteroides	strain=ATCC 33313	GCA_000160575.1	1249	1249	type	True	78.4998	64	568	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	78.2768	59	568	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	78.2521	63	568	95	below_threshold
Weissella minor	strain=DSM 20014	GCA_001437425.1	1620	1620	type	True	77.889	73	568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:03,962] [INFO] DFAST Taxonomy check result was written to GCF_000277645.1_ASM27764v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:03,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:03,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:03,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/checkm_data
[2024-01-24 13:10:03,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:04,003] [INFO] Task started: CheckM
[2024-01-24 13:10:04,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000277645.1_ASM27764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000277645.1_ASM27764v1_genomic.fna/checkm_input GCF_000277645.1_ASM27764v1_genomic.fna/checkm_result
[2024-01-24 13:10:22,982] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:22,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,000] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:23,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:23,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000277645.1_ASM27764v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:23,002] [INFO] Task started: Blastn
[2024-01-24 13:10:23,002] [INFO] Running command: blastn -query GCF_000277645.1_ASM27764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda9e27f0-460d-4281-a247-ae4b2b71696f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000277645.1_ASM27764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:23,843] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:23,846] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:23,846] [INFO] Target genome list was writen to GCF_000277645.1_ASM27764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:23,857] [INFO] Task started: fastANI
[2024-01-24 13:10:23,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgff9fee93-df60-4c99-8b97-1d475eefaaa5/GCF_000277645.1_ASM27764v1_genomic.fna.gz --refList GCF_000277645.1_ASM27764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000277645.1_ASM27764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:30,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:30,344] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:30,345] [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_000277645.1	s__Weissella koreensis	100.0	532	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	conclusive
GCF_011304355.1	s__Weissella coleopterorum	81.8971	316	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006777025.1	s__Weissella hellenica_B	80.4292	83	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.22	98.80	0.93	0.90	9	-
GCF_014397255.1	s__Weissella diestrammenae	80.1786	110	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018394055.1	s__Weissella ceti	80.1268	56	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438705.1	s__Weissella kandleri	78.7746	136	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193635.1	s__Weissella cibaria	78.6777	51	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_000160575.1	s__Weissella paramesenteroides	78.4998	64	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.27	97.99	0.88	0.85	25	-
GCF_000691805.2	s__Weissella oryzae	78.259	58	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437355.1	s__Weissella viridescens	78.1937	64	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.44	98.29	0.96	0.91	6	-
GCF_001437425.1	s__Weissella minor	77.889	73	568	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:30,346] [INFO] GTDB search result was written to GCF_000277645.1_ASM27764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:30,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:30,350] [INFO] DFAST_QC result json was written to GCF_000277645.1_ASM27764v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:30,350] [INFO] DFAST_QC completed!
[2024-01-24 13:10:30,350] [INFO] Total running time: 0h0m39s