[2024-01-24 14:14:05,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:05,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:05,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference
[2024-01-24 14:14:06,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:06,690] [INFO] Task started: Prodigal
[2024-01-24 14:14:06,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf6495e9-a596-4e9e-8296-a5eb9cded06e/GCF_014397255.1_ASM1439725v1_genomic.fna.gz | prodigal -d GCF_014397255.1_ASM1439725v1_genomic.fna/cds.fna -a GCF_014397255.1_ASM1439725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:11,046] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:11,046] [INFO] Task started: HMMsearch
[2024-01-24 14:14:11,046] [INFO] Running command: hmmsearch --tblout GCF_014397255.1_ASM1439725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/reference_markers.hmm GCF_014397255.1_ASM1439725v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:11,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:11,292] [INFO] Found 6/6 markers.
[2024-01-24 14:14:11,322] [INFO] Query marker FASTA was written to GCF_014397255.1_ASM1439725v1_genomic.fna/markers.fasta
[2024-01-24 14:14:11,323] [INFO] Task started: Blastn
[2024-01-24 14:14:11,323] [INFO] Running command: blastn -query GCF_014397255.1_ASM1439725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/reference_markers.fasta -out GCF_014397255.1_ASM1439725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:11,994] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:11,997] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:11,997] [INFO] Target genome list was writen to GCF_014397255.1_ASM1439725v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:12,009] [INFO] Task started: fastANI
[2024-01-24 14:14:12,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6495e9-a596-4e9e-8296-a5eb9cded06e/GCF_014397255.1_ASM1439725v1_genomic.fna.gz --refList GCF_014397255.1_ASM1439725v1_genomic.fna/target_genomes.txt --output GCF_014397255.1_ASM1439725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:18,752] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:18,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:18,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:18,761] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:18,761] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:18,762] [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 diestrammenae	strain=KACC 16890	GCA_014397255.1	1162633	1162633	type	True	100.0	552	553	95	conclusive
Weissella coleopterorum	strain=HDW19	GCA_011304355.1	2714949	2714949	type	True	80.0471	105	553	95	below_threshold
Weissella koreensis	strain=KCTC 3621	GCA_000277645.1	165096	165096	type	True	79.8677	107	553	95	below_threshold
Weissella kandleri	strain=DSM 20593	GCA_001438705.1	1616	1616	type	True	79.1242	90	553	95	below_threshold
Weissella sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	78.7273	72	553	95	below_threshold
Weissella bombi	strain=DSM 28794	GCA_005405505.1	1505725	1505725	type	True	78.3114	66	553	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	78.2579	67	553	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	77.4968	71	553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:18,764] [INFO] DFAST Taxonomy check result was written to GCF_014397255.1_ASM1439725v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:18,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:18,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:18,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/checkm_data
[2024-01-24 14:14:18,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:18,817] [INFO] Task started: CheckM
[2024-01-24 14:14:18,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014397255.1_ASM1439725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014397255.1_ASM1439725v1_genomic.fna/checkm_input GCF_014397255.1_ASM1439725v1_genomic.fna/checkm_result
[2024-01-24 14:14:38,424] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:38,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:38,445] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:38,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:38,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014397255.1_ASM1439725v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:38,447] [INFO] Task started: Blastn
[2024-01-24 14:14:38,447] [INFO] Running command: blastn -query GCF_014397255.1_ASM1439725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a38460-1187-4862-ad8d-903c4223e458/dqc_reference/reference_markers_gtdb.fasta -out GCF_014397255.1_ASM1439725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:39,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:39,319] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:39,320] [INFO] Target genome list was writen to GCF_014397255.1_ASM1439725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:39,342] [INFO] Task started: fastANI
[2024-01-24 14:14:39,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf6495e9-a596-4e9e-8296-a5eb9cded06e/GCF_014397255.1_ASM1439725v1_genomic.fna.gz --refList GCF_014397255.1_ASM1439725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014397255.1_ASM1439725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:45,486] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:45,499] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:45,499] [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_014397255.1	s__Weissella diestrammenae	100.0	553	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000277645.1	s__Weissella koreensis	80.1316	107	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_011304355.1	s__Weissella coleopterorum	80.0035	105	553	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	79.8232	82	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.22	98.80	0.93	0.90	9	-
GCF_001438705.1	s__Weissella kandleri	79.1242	90	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003862435.1	s__Weissella viridescens_A	78.2773	56	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094835.1	s__Weissella bombi	78.2497	66	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000691805.2	s__Weissella oryzae	78.2491	57	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405545.1	s__Weissella hellenica	77.6428	73	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	99.99	0.99	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:45,501] [INFO] GTDB search result was written to GCF_014397255.1_ASM1439725v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:45,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:45,506] [INFO] DFAST_QC result json was written to GCF_014397255.1_ASM1439725v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:45,507] [INFO] DFAST_QC completed!
[2024-01-24 14:14:45,507] [INFO] Total running time: 0h0m40s