[2024-01-24 12:40:50,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference
[2024-01-24 12:40:51,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,918] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg1716c344-528e-468d-b6af-6414df4e713a/GCF_000372485.1_ASM37248v1_genomic.fna.gz | prodigal -d GCF_000372485.1_ASM37248v1_genomic.fna/cds.fna -a GCF_000372485.1_ASM37248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:55,648] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:55,649] [INFO] Task started: HMMsearch
[2024-01-24 12:40:55,649] [INFO] Running command: hmmsearch --tblout GCF_000372485.1_ASM37248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/reference_markers.hmm GCF_000372485.1_ASM37248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:55,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:55,851] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1716c344-528e-468d-b6af-6414df4e713a/GCF_000372485.1_ASM37248v1_genomic.fna.gz]
[2024-01-24 12:40:55,876] [INFO] Query marker FASTA was written to GCF_000372485.1_ASM37248v1_genomic.fna/markers.fasta
[2024-01-24 12:40:55,877] [INFO] Task started: Blastn
[2024-01-24 12:40:55,877] [INFO] Running command: blastn -query GCF_000372485.1_ASM37248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/reference_markers.fasta -out GCF_000372485.1_ASM37248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:56,444] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:56,450] [INFO] Selected 20 target genomes.
[2024-01-24 12:40:56,450] [INFO] Target genome list was writen to GCF_000372485.1_ASM37248v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:56,460] [INFO] Task started: fastANI
[2024-01-24 12:40:56,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg1716c344-528e-468d-b6af-6414df4e713a/GCF_000372485.1_ASM37248v1_genomic.fna.gz --refList GCF_000372485.1_ASM37248v1_genomic.fna/target_genomes.txt --output GCF_000372485.1_ASM37248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:04,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:04,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:04,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:04,321] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:41:04,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:04,322] [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
Oenococcus oeni	strain=DSM 20252	GCA_000372485.1	1247	1247	type	True	100.0	564	566	95	conclusive
Oenococcus oeni	strain=DSM 20252	GCA_000309445.1	1247	1247	type	True	99.9581	551	566	95	conclusive
Oenococcus kitaharae	strain=DSM 17330	GCA_000428085.1	336988	336988	type	True	78.4224	127	566	95	below_threshold
Oenococcus kitaharae	strain=DSM 17330	GCA_000241055.1	336988	336988	type	True	78.2943	131	566	95	below_threshold
Oenococcus sicerae	strain=UCMA 15228	GCA_004102045.2	2203724	2203724	type	True	78.2081	163	566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:04,323] [INFO] DFAST Taxonomy check result was written to GCF_000372485.1_ASM37248v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:04,324] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:04,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:04,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/checkm_data
[2024-01-24 12:41:04,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:04,350] [INFO] Task started: CheckM
[2024-01-24 12:41:04,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372485.1_ASM37248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372485.1_ASM37248v1_genomic.fna/checkm_input GCF_000372485.1_ASM37248v1_genomic.fna/checkm_result
[2024-01-24 12:41:22,944] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:22,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:22,967] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:22,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:22,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372485.1_ASM37248v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:22,968] [INFO] Task started: Blastn
[2024-01-24 12:41:22,969] [INFO] Running command: blastn -query GCF_000372485.1_ASM37248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8195272-384c-4104-9fdc-868e63e9cb0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372485.1_ASM37248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:23,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:23,695] [INFO] Selected 17 target genomes.
[2024-01-24 12:41:23,695] [INFO] Target genome list was writen to GCF_000372485.1_ASM37248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:23,706] [INFO] Task started: fastANI
[2024-01-24 12:41:23,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg1716c344-528e-468d-b6af-6414df4e713a/GCF_000372485.1_ASM37248v1_genomic.fna.gz --refList GCF_000372485.1_ASM37248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372485.1_ASM37248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:31,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:31,139] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:31,139] [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_000372485.1	s__Oenococcus oeni	100.0	565	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	99.45	98.41	0.93	0.87	237	conclusive
GCF_004010835.2	s__Oenococcus sp004010835	87.0134	500	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241055.1	s__Oenococcus kitaharae	78.2943	131	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	99.96	99.86	0.99	0.98	5	-
GCF_004102045.2	s__Oenococcus sicerae	78.0913	162	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	98.32	98.32	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:31,141] [INFO] GTDB search result was written to GCF_000372485.1_ASM37248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:31,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:31,146] [INFO] DFAST_QC result json was written to GCF_000372485.1_ASM37248v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:31,146] [INFO] DFAST_QC completed!
[2024-01-24 12:41:31,146] [INFO] Total running time: 0h0m40s