[2024-01-24 12:16:08,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,364] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference
[2024-01-24 12:16:09,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,705] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg46a668b7-a680-4ef1-8a85-2333db2b09f3/GCF_900478045.1_47555_C02_genomic.fna.gz | prodigal -d GCF_900478045.1_47555_C02_genomic.fna/cds.fna -a GCF_900478045.1_47555_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:18,696] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:18,696] [INFO] Task started: HMMsearch
[2024-01-24 12:16:18,696] [INFO] Running command: hmmsearch --tblout GCF_900478045.1_47555_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/reference_markers.hmm GCF_900478045.1_47555_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:18,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:18,925] [INFO] Found 6/6 markers.
[2024-01-24 12:16:18,956] [INFO] Query marker FASTA was written to GCF_900478045.1_47555_C02_genomic.fna/markers.fasta
[2024-01-24 12:16:18,957] [INFO] Task started: Blastn
[2024-01-24 12:16:18,957] [INFO] Running command: blastn -query GCF_900478045.1_47555_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/reference_markers.fasta -out GCF_900478045.1_47555_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:19,819] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:19,823] [INFO] Selected 5 target genomes.
[2024-01-24 12:16:19,824] [INFO] Target genome list was writen to GCF_900478045.1_47555_C02_genomic.fna/target_genomes.txt
[2024-01-24 12:16:19,840] [INFO] Task started: fastANI
[2024-01-24 12:16:19,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a668b7-a680-4ef1-8a85-2333db2b09f3/GCF_900478045.1_47555_C02_genomic.fna.gz --refList GCF_900478045.1_47555_C02_genomic.fna/target_genomes.txt --output GCF_900478045.1_47555_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:23,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:23,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:23,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:23,417] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:16:23,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:23,417] [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 minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	100.0	898	898	95	conclusive
Corynebacterium minutissimum	strain=FDAARGOS_894	GCA_016027615.1	38301	38301	type	True	99.9999	897	898	95	conclusive
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	99.9767	869	898	95	conclusive
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	99.9757	865	898	95	conclusive
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	85.373	729	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:23,419] [INFO] DFAST Taxonomy check result was written to GCF_900478045.1_47555_C02_genomic.fna/tc_result.tsv
[2024-01-24 12:16:23,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:23,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:23,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/checkm_data
[2024-01-24 12:16:23,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:23,452] [INFO] Task started: CheckM
[2024-01-24 12:16:23,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900478045.1_47555_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900478045.1_47555_C02_genomic.fna/checkm_input GCF_900478045.1_47555_C02_genomic.fna/checkm_result
[2024-01-24 12:16:53,540] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:53,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:53,562] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:53,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:53,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900478045.1_47555_C02_genomic.fna/markers.fasta)
[2024-01-24 12:16:53,563] [INFO] Task started: Blastn
[2024-01-24 12:16:53,563] [INFO] Running command: blastn -query GCF_900478045.1_47555_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b7018fe-e297-4fb5-8a2a-c478e67d865e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900478045.1_47555_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:54,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:54,873] [INFO] Selected 8 target genomes.
[2024-01-24 12:16:54,873] [INFO] Target genome list was writen to GCF_900478045.1_47555_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:54,880] [INFO] Task started: fastANI
[2024-01-24 12:16:54,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg46a668b7-a680-4ef1-8a85-2333db2b09f3/GCF_900478045.1_47555_C02_genomic.fna.gz --refList GCF_900478045.1_47555_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900478045.1_47555_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:00,721] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:00,737] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:00,737] [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_000805675.1	s__Corynebacterium minutissimum	99.9767	869	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	conclusive
GCF_016889765.1	s__Corynebacterium minutissimum_B	94.1166	809	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_001812805.1	s__Corynebacterium sp001812805	93.5082	787	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833575.1	s__Corynebacterium singulare	85.373	729	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.05	96.95	0.89	0.88	3	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	84.5305	698	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	84.3188	669	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_016728705.1	s__Corynebacterium sp001807205	84.2594	673	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_000022905.1	s__Corynebacterium aurimucosum	84.2275	686	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:00,739] [INFO] GTDB search result was written to GCF_900478045.1_47555_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:00,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:00,743] [INFO] DFAST_QC result json was written to GCF_900478045.1_47555_C02_genomic.fna/dqc_result.json
[2024-01-24 12:17:00,743] [INFO] DFAST_QC completed!
[2024-01-24 12:17:00,743] [INFO] Total running time: 0h0m52s