[2024-01-24 14:22:17,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference
[2024-01-24 14:22:18,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,391] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,391] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bb9772d-87b5-48e8-a368-89f536a0244e/GCF_016027615.1_ASM1602761v1_genomic.fna.gz | prodigal -d GCF_016027615.1_ASM1602761v1_genomic.fna/cds.fna -a GCF_016027615.1_ASM1602761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:27,359] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:27,360] [INFO] Task started: HMMsearch
[2024-01-24 14:22:27,360] [INFO] Running command: hmmsearch --tblout GCF_016027615.1_ASM1602761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/reference_markers.hmm GCF_016027615.1_ASM1602761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:27,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:27,601] [INFO] Found 6/6 markers.
[2024-01-24 14:22:27,637] [INFO] Query marker FASTA was written to GCF_016027615.1_ASM1602761v1_genomic.fna/markers.fasta
[2024-01-24 14:22:27,638] [INFO] Task started: Blastn
[2024-01-24 14:22:27,638] [INFO] Running command: blastn -query GCF_016027615.1_ASM1602761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/reference_markers.fasta -out GCF_016027615.1_ASM1602761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:28,532] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:28,537] [INFO] Selected 5 target genomes.
[2024-01-24 14:22:28,537] [INFO] Target genome list was writen to GCF_016027615.1_ASM1602761v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:28,542] [INFO] Task started: fastANI
[2024-01-24 14:22:28,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb9772d-87b5-48e8-a368-89f536a0244e/GCF_016027615.1_ASM1602761v1_genomic.fna.gz --refList GCF_016027615.1_ASM1602761v1_genomic.fna/target_genomes.txt --output GCF_016027615.1_ASM1602761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:32,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:32,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:32,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:32,139] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:22:32,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:32,140] [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=FDAARGOS_894	GCA_016027615.1	38301	38301	type	True	100.0	898	898	95	conclusive
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	99.9999	897	898	95	conclusive
Corynebacterium minutissimum	strain=NBRC 15361	GCA_001552395.1	38301	38301	type	True	99.9779	867	898	95	conclusive
Corynebacterium minutissimum	strain=ATCC 23348	GCA_000805675.1	38301	38301	type	True	99.9608	867	898	95	conclusive
Corynebacterium singulare	strain=IBS B52218	GCA_000833575.1	161899	161899	type	True	85.3371	732	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:32,144] [INFO] DFAST Taxonomy check result was written to GCF_016027615.1_ASM1602761v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:32,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:32,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:32,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/checkm_data
[2024-01-24 14:22:32,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:32,179] [INFO] Task started: CheckM
[2024-01-24 14:22:32,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027615.1_ASM1602761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027615.1_ASM1602761v1_genomic.fna/checkm_input GCF_016027615.1_ASM1602761v1_genomic.fna/checkm_result
[2024-01-24 14:23:02,367] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:02,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:02,385] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:02,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:02,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027615.1_ASM1602761v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:02,386] [INFO] Task started: Blastn
[2024-01-24 14:23:02,386] [INFO] Running command: blastn -query GCF_016027615.1_ASM1602761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3019ca91-17be-4b33-9f96-0c2878c1850f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027615.1_ASM1602761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:03,635] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:03,639] [INFO] Selected 8 target genomes.
[2024-01-24 14:23:03,639] [INFO] Target genome list was writen to GCF_016027615.1_ASM1602761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:03,646] [INFO] Task started: fastANI
[2024-01-24 14:23:03,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb9772d-87b5-48e8-a368-89f536a0244e/GCF_016027615.1_ASM1602761v1_genomic.fna.gz --refList GCF_016027615.1_ASM1602761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027615.1_ASM1602761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:09,452] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:09,460] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:09,460] [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	99.9608	867	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	94.2094	803	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	93.4265	794	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	85.3437	734	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	84.585	682	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	84.5184	657	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_000022905.1	s__Corynebacterium aurimucosum	84.419	677	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_016728705.1	s__Corynebacterium sp001807205	84.3151	670	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:09,461] [INFO] GTDB search result was written to GCF_016027615.1_ASM1602761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:09,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:09,464] [INFO] DFAST_QC result json was written to GCF_016027615.1_ASM1602761v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:09,464] [INFO] DFAST_QC completed!
[2024-01-24 14:23:09,464] [INFO] Total running time: 0h0m52s