[2024-01-25 18:54:05,635] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:05,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:05,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference
[2024-01-25 18:54:06,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:06,884] [INFO] Task started: Prodigal
[2024-01-25 18:54:06,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfdb13fa-8f7f-42bb-8297-0a270470ab05/GCF_004136195.1_ASM413619v1_genomic.fna.gz | prodigal -d GCF_004136195.1_ASM413619v1_genomic.fna/cds.fna -a GCF_004136195.1_ASM413619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:13,844] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:13,845] [INFO] Task started: HMMsearch
[2024-01-25 18:54:13,845] [INFO] Running command: hmmsearch --tblout GCF_004136195.1_ASM413619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/reference_markers.hmm GCF_004136195.1_ASM413619v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:14,018] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:14,019] [INFO] Found 6/6 markers.
[2024-01-25 18:54:14,043] [INFO] Query marker FASTA was written to GCF_004136195.1_ASM413619v1_genomic.fna/markers.fasta
[2024-01-25 18:54:14,043] [INFO] Task started: Blastn
[2024-01-25 18:54:14,043] [INFO] Running command: blastn -query GCF_004136195.1_ASM413619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/reference_markers.fasta -out GCF_004136195.1_ASM413619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:14,795] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:14,798] [INFO] Selected 10 target genomes.
[2024-01-25 18:54:14,798] [INFO] Target genome list was writen to GCF_004136195.1_ASM413619v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:14,810] [INFO] Task started: fastANI
[2024-01-25 18:54:14,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfdb13fa-8f7f-42bb-8297-0a270470ab05/GCF_004136195.1_ASM413619v1_genomic.fna.gz --refList GCF_004136195.1_ASM413619v1_genomic.fna/target_genomes.txt --output GCF_004136195.1_ASM413619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:23,403] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:23,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:23,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:23,418] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:54:23,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:23,418] [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
Cutibacterium acnes	strain=DSM 1897	GCA_004136195.1	1747	1747	type	True	100.0	828	831	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	99.9995	828	831	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	99.9984	830	831	95	conclusive
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	99.9944	819	831	95	conclusive
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	99.9457	778	831	95	conclusive
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.8235	55	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:23,420] [INFO] DFAST Taxonomy check result was written to GCF_004136195.1_ASM413619v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:23,420] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:23,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:23,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/checkm_data
[2024-01-25 18:54:23,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:23,448] [INFO] Task started: CheckM
[2024-01-25 18:54:23,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004136195.1_ASM413619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004136195.1_ASM413619v1_genomic.fna/checkm_input GCF_004136195.1_ASM413619v1_genomic.fna/checkm_result
[2024-01-25 18:54:49,147] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:49,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:49,166] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:49,166] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:49,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004136195.1_ASM413619v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:49,167] [INFO] Task started: Blastn
[2024-01-25 18:54:49,167] [INFO] Running command: blastn -query GCF_004136195.1_ASM413619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88916aed-c9ca-4402-8274-17fd0c29561a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004136195.1_ASM413619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:50,334] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:50,336] [INFO] Selected 6 target genomes.
[2024-01-25 18:54:50,336] [INFO] Target genome list was writen to GCF_004136195.1_ASM413619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:50,348] [INFO] Task started: fastANI
[2024-01-25 18:54:50,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfdb13fa-8f7f-42bb-8297-0a270470ab05/GCF_004136195.1_ASM413619v1_genomic.fna.gz --refList GCF_004136195.1_ASM413619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004136195.1_ASM413619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:54,315] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:54,320] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:54,320] [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_003030305.1	s__Cutibacterium acnes	99.9995	829	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	conclusive
GCF_001642025.1	s__Cutibacterium namnetense	88.3009	699	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_008326345.1	s__Cutibacterium modestum	85.9067	722	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	-
GCF_009696315.1	s__Cutibacterium porci	82.6966	615	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000227295.1	s__Cutibacterium avidum	81.577	581	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	78.4062	213	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:54,322] [INFO] GTDB search result was written to GCF_004136195.1_ASM413619v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:54,322] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:54,328] [INFO] DFAST_QC result json was written to GCF_004136195.1_ASM413619v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:54,328] [INFO] DFAST_QC completed!
[2024-01-25 18:54:54,328] [INFO] Total running time: 0h0m49s