[2024-01-25 18:06:05,781] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference
[2024-01-25 18:06:06,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,906] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg72cf52e1-fdd9-43a1-aa01-8f82c58a8a71/GCF_018394055.1_ASM1839405v1_genomic.fna.gz | prodigal -d GCF_018394055.1_ASM1839405v1_genomic.fna/cds.fna -a GCF_018394055.1_ASM1839405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:10,230] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:10,231] [INFO] Task started: HMMsearch
[2024-01-25 18:06:10,231] [INFO] Running command: hmmsearch --tblout GCF_018394055.1_ASM1839405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/reference_markers.hmm GCF_018394055.1_ASM1839405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:10,411] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:10,412] [INFO] Found 6/6 markers.
[2024-01-25 18:06:10,429] [INFO] Query marker FASTA was written to GCF_018394055.1_ASM1839405v1_genomic.fna/markers.fasta
[2024-01-25 18:06:10,429] [INFO] Task started: Blastn
[2024-01-25 18:06:10,429] [INFO] Running command: blastn -query GCF_018394055.1_ASM1839405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/reference_markers.fasta -out GCF_018394055.1_ASM1839405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:10,966] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:10,969] [INFO] Selected 17 target genomes.
[2024-01-25 18:06:10,969] [INFO] Target genome list was writen to GCF_018394055.1_ASM1839405v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:10,975] [INFO] Task started: fastANI
[2024-01-25 18:06:10,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg72cf52e1-fdd9-43a1-aa01-8f82c58a8a71/GCF_018394055.1_ASM1839405v1_genomic.fna.gz --refList GCF_018394055.1_ASM1839405v1_genomic.fna/target_genomes.txt --output GCF_018394055.1_ASM1839405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:16,010] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:16,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:16,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:16,017] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:16,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:16,018] [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 ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	100.0	499	501	95	conclusive
Weissella coleopterorum	strain=HDW19	GCA_011304355.1	2714949	2714949	type	True	80.3971	52	501	95	below_threshold
Weissella jogaejeotgali	strain=FOL01	GCA_001932615.1	1631871	1631871	type	True	80.0401	71	501	95	below_threshold
Weissella viridescens	strain=NCTC13645	GCA_900460455.1	1629	1629	type	True	79.7624	106	501	95	below_threshold
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	79.472	102	501	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	79.387	107	501	95	below_threshold
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	78.9883	98	501	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	78.9254	103	501	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	78.7498	76	501	95	below_threshold
Weissella bombi	strain=DSM 28794	GCA_005405505.1	1505725	1505725	type	True	78.5891	78	501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:16,019] [INFO] DFAST Taxonomy check result was written to GCF_018394055.1_ASM1839405v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:16,020] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:16,020] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:16,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/checkm_data
[2024-01-25 18:06:16,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:16,037] [INFO] Task started: CheckM
[2024-01-25 18:06:16,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018394055.1_ASM1839405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018394055.1_ASM1839405v1_genomic.fna/checkm_input GCF_018394055.1_ASM1839405v1_genomic.fna/checkm_result
[2024-01-25 18:06:32,077] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:32,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:32,096] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:32,096] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:32,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018394055.1_ASM1839405v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:32,097] [INFO] Task started: Blastn
[2024-01-25 18:06:32,097] [INFO] Running command: blastn -query GCF_018394055.1_ASM1839405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c04dee0-cef1-4d27-a173-2834cf9f6f67/dqc_reference/reference_markers_gtdb.fasta -out GCF_018394055.1_ASM1839405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:32,816] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:32,818] [INFO] Selected 14 target genomes.
[2024-01-25 18:06:32,818] [INFO] Target genome list was writen to GCF_018394055.1_ASM1839405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:32,828] [INFO] Task started: fastANI
[2024-01-25 18:06:32,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg72cf52e1-fdd9-43a1-aa01-8f82c58a8a71/GCF_018394055.1_ASM1839405v1_genomic.fna.gz --refList GCF_018394055.1_ASM1839405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018394055.1_ASM1839405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:37,717] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:37,725] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:37,725] [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_018394055.1	s__Weissella ceti	100.0	498	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000750535.1	s__Weissella ceti_A	83.9594	303	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.87	99.79	0.99	0.98	5	-
GCF_004771295.1	s__Weissella confusa_B	80.4313	137	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCF_011304355.1	s__Weissella coleopterorum	80.2378	51	501	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	79.8378	121	501	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	79.496	129	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_000193635.1	s__Weissella cibaria	79.4003	104	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_001437425.1	s__Weissella minor	79.3201	118	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
GCF_003862435.1	s__Weissella viridescens_A	79.272	116	501	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	78.9254	103	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.44	98.29	0.96	0.91	6	-
GCF_900094835.1	s__Weissella bombi	78.7519	75	501	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:37,726] [INFO] GTDB search result was written to GCF_018394055.1_ASM1839405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:37,726] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:37,729] [INFO] DFAST_QC result json was written to GCF_018394055.1_ASM1839405v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:37,729] [INFO] DFAST_QC completed!
[2024-01-25 18:06:37,729] [INFO] Total running time: 0h0m32s