[2024-01-24 12:44:11,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,049] [INFO] DQC Reference Directory: /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference
[2024-01-24 12:44:12,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,368] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,368] [INFO] Running command: gunzip -c /var/lib/cwl/stge7282dce-d533-4895-a823-7d781c9c0174/GCF_900637605.1_52121_H02_genomic.fna.gz | prodigal -d GCF_900637605.1_52121_H02_genomic.fna/cds.fna -a GCF_900637605.1_52121_H02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:18,159] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:18,160] [INFO] Task started: HMMsearch
[2024-01-24 12:44:18,160] [INFO] Running command: hmmsearch --tblout GCF_900637605.1_52121_H02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/reference_markers.hmm GCF_900637605.1_52121_H02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:18,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:18,455] [INFO] Found 6/6 markers.
[2024-01-24 12:44:18,478] [INFO] Query marker FASTA was written to GCF_900637605.1_52121_H02_genomic.fna/markers.fasta
[2024-01-24 12:44:18,479] [INFO] Task started: Blastn
[2024-01-24 12:44:18,479] [INFO] Running command: blastn -query GCF_900637605.1_52121_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/reference_markers.fasta -out GCF_900637605.1_52121_H02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:19,145] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:19,148] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:19,149] [INFO] Target genome list was writen to GCF_900637605.1_52121_H02_genomic.fna/target_genomes.txt
[2024-01-24 12:44:19,259] [INFO] Task started: fastANI
[2024-01-24 12:44:19,259] [INFO] Running command: fastANI --query /var/lib/cwl/stge7282dce-d533-4895-a823-7d781c9c0174/GCF_900637605.1_52121_H02_genomic.fna.gz --refList GCF_900637605.1_52121_H02_genomic.fna/target_genomes.txt --output GCF_900637605.1_52121_H02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:24,390] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:24,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:24,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:24,398] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:24,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:24,398] [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 kutscheri	strain=NCTC11138	GCA_900637605.1	35755	35755	type	True	100.0	781	784	95	conclusive
Corynebacterium kutscheri	strain=DSM 20755	GCA_000980835.1	35755	35755	type	True	99.9983	780	784	95	conclusive
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	80.0636	83	784	95	below_threshold
Corynebacterium rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	79.6382	78	784	95	below_threshold
Corynebacterium pseudotuberculosis	strain=DSM 20689	GCA_003634885.1	1719	1719	type	True	79.1584	75	784	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	78.7553	73	784	95	below_threshold
Corynebacterium pseudotuberculosis	strain=ATCC 19410	GCA_002155265.1	1719	1719	type	True	78.6116	77	784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:24,401] [INFO] DFAST Taxonomy check result was written to GCF_900637605.1_52121_H02_genomic.fna/tc_result.tsv
[2024-01-24 12:44:24,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:24,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:24,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/checkm_data
[2024-01-24 12:44:24,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:24,432] [INFO] Task started: CheckM
[2024-01-24 12:44:24,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637605.1_52121_H02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637605.1_52121_H02_genomic.fna/checkm_input GCF_900637605.1_52121_H02_genomic.fna/checkm_result
[2024-01-24 12:44:48,622] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:48,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:48,643] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:48,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:48,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637605.1_52121_H02_genomic.fna/markers.fasta)
[2024-01-24 12:44:48,644] [INFO] Task started: Blastn
[2024-01-24 12:44:48,645] [INFO] Running command: blastn -query GCF_900637605.1_52121_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b8d715-737f-4327-a8cc-350fac3f581b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637605.1_52121_H02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:49,466] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:49,470] [INFO] Selected 19 target genomes.
[2024-01-24 12:44:49,471] [INFO] Target genome list was writen to GCF_900637605.1_52121_H02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:49,504] [INFO] Task started: fastANI
[2024-01-24 12:44:49,504] [INFO] Running command: fastANI --query /var/lib/cwl/stge7282dce-d533-4895-a823-7d781c9c0174/GCF_900637605.1_52121_H02_genomic.fna.gz --refList GCF_900637605.1_52121_H02_genomic.fna/target_genomes_gtdb.txt --output GCF_900637605.1_52121_H02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:56,856] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:56,865] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:56,865] [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_000980835.1	s__Corynebacterium kutscheri	99.9983	780	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	99.55	0.99	0.98	4	conclusive
GCF_001457455.1	s__Corynebacterium diphtheriae	79.9159	83	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_902702935.1	s__Corynebacterium rouxii	79.4492	77	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187135.1	s__Corynebacterium ulcerans	79.3862	79	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_001020985.1	s__Corynebacterium mustelae	79.2876	75	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155265.1	s__Corynebacterium pseudotuberculosis	78.9301	78	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.58	98.61	0.99	0.97	131	-
GCF_004382825.2	s__Corynebacterium silvaticum	78.3683	73	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_007904105.1	s__Corynebacterium sp007904105	78.0269	77	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.94	98.94	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:56,868] [INFO] GTDB search result was written to GCF_900637605.1_52121_H02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:56,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:56,872] [INFO] DFAST_QC result json was written to GCF_900637605.1_52121_H02_genomic.fna/dqc_result.json
[2024-01-24 12:44:56,873] [INFO] DFAST_QC completed!
[2024-01-24 12:44:56,873] [INFO] Total running time: 0h0m46s