[2024-01-24 14:06:29,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,651] [INFO] DQC Reference Directory: /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference
[2024-01-24 14:06:31,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,030] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg792da172-0df3-48d2-89b8-6777b36623f3/GCF_004382825.2_ASM438282v2_genomic.fna.gz | prodigal -d GCF_004382825.2_ASM438282v2_genomic.fna/cds.fna -a GCF_004382825.2_ASM438282v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:38,968] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:38,968] [INFO] Task started: HMMsearch
[2024-01-24 14:06:38,969] [INFO] Running command: hmmsearch --tblout GCF_004382825.2_ASM438282v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/reference_markers.hmm GCF_004382825.2_ASM438282v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:39,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:39,245] [INFO] Found 6/6 markers.
[2024-01-24 14:06:39,272] [INFO] Query marker FASTA was written to GCF_004382825.2_ASM438282v2_genomic.fna/markers.fasta
[2024-01-24 14:06:39,272] [INFO] Task started: Blastn
[2024-01-24 14:06:39,273] [INFO] Running command: blastn -query GCF_004382825.2_ASM438282v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/reference_markers.fasta -out GCF_004382825.2_ASM438282v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:40,062] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:40,066] [INFO] Selected 7 target genomes.
[2024-01-24 14:06:40,066] [INFO] Target genome list was writen to GCF_004382825.2_ASM438282v2_genomic.fna/target_genomes.txt
[2024-01-24 14:06:40,070] [INFO] Task started: fastANI
[2024-01-24 14:06:40,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg792da172-0df3-48d2-89b8-6777b36623f3/GCF_004382825.2_ASM438282v2_genomic.fna.gz --refList GCF_004382825.2_ASM438282v2_genomic.fna/target_genomes.txt --output GCF_004382825.2_ASM438282v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:44,281] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:44,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:44,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:44,288] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:44,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:44,289] [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
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	100.0	847	847	95	conclusive
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	91.1336	757	847	95	below_threshold
Corynebacterium ulcerans	strain=FDAARGOS_1118	GCA_016727365.1	65058	65058	type	True	91.0573	766	847	95	below_threshold
Corynebacterium pseudotuberculosis	strain=ATCC 19410	GCA_002155265.1	1719	1719	type	True	85.5507	705	847	95	below_threshold
Corynebacterium pseudotuberculosis	strain=DSM 20689	GCA_003634885.1	1719	1719	type	True	85.5161	708	847	95	below_threshold
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	78.0081	85	847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,291] [INFO] DFAST Taxonomy check result was written to GCF_004382825.2_ASM438282v2_genomic.fna/tc_result.tsv
[2024-01-24 14:06:44,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:44,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:44,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/checkm_data
[2024-01-24 14:06:44,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:44,322] [INFO] Task started: CheckM
[2024-01-24 14:06:44,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004382825.2_ASM438282v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004382825.2_ASM438282v2_genomic.fna/checkm_input GCF_004382825.2_ASM438282v2_genomic.fna/checkm_result
[2024-01-24 14:07:13,754] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:13,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,780] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:13,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:13,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004382825.2_ASM438282v2_genomic.fna/markers.fasta)
[2024-01-24 14:07:13,781] [INFO] Task started: Blastn
[2024-01-24 14:07:13,781] [INFO] Running command: blastn -query GCF_004382825.2_ASM438282v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge9eb6803-e103-4538-b521-9060ad509495/dqc_reference/reference_markers_gtdb.fasta -out GCF_004382825.2_ASM438282v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:14,733] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:14,736] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:14,737] [INFO] Target genome list was writen to GCF_004382825.2_ASM438282v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:14,747] [INFO] Task started: fastANI
[2024-01-24 14:07:14,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg792da172-0df3-48d2-89b8-6777b36623f3/GCF_004382825.2_ASM438282v2_genomic.fna.gz --refList GCF_004382825.2_ASM438282v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004382825.2_ASM438282v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:20,355] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:20,364] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:20,364] [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_004382825.2	s__Corynebacterium silvaticum	100.0	847	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	conclusive
GCF_900187135.1	s__Corynebacterium ulcerans	91.1336	757	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_002155265.1	s__Corynebacterium pseudotuberculosis	85.5507	705	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.58	98.61	0.99	0.97	131	-
GCF_902702935.1	s__Corynebacterium rouxii	79.2557	178	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457455.1	s__Corynebacterium diphtheriae	79.1471	163	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_002355155.1	s__Corynebacterium suranareeae	77.9671	86	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734385.1	s__Corynebacterium sp009734385	77.8085	85	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001875725.1	s__Corynebacterium sp001875725	77.7123	65	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143825.1	s__Corynebacterium genitalium_A	77.4628	64	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014267345.1	s__Corynebacterium sp014267345	77.288	79	847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:20,375] [INFO] GTDB search result was written to GCF_004382825.2_ASM438282v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:20,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:20,380] [INFO] DFAST_QC result json was written to GCF_004382825.2_ASM438282v2_genomic.fna/dqc_result.json
[2024-01-24 14:07:20,381] [INFO] DFAST_QC completed!
[2024-01-24 14:07:20,381] [INFO] Total running time: 0h0m51s