[2024-01-24 13:03:20,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference
[2024-01-24 13:03:21,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,955] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,955] [INFO] Running command: gunzip -c /var/lib/cwl/stg492c638e-8cd8-454d-b9bc-fb51b78ccdef/GCF_000732945.1_ASM73294v1_genomic.fna.gz | prodigal -d GCF_000732945.1_ASM73294v1_genomic.fna/cds.fna -a GCF_000732945.1_ASM73294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:28,979] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:28,980] [INFO] Task started: HMMsearch
[2024-01-24 13:03:28,980] [INFO] Running command: hmmsearch --tblout GCF_000732945.1_ASM73294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/reference_markers.hmm GCF_000732945.1_ASM73294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:29,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:29,214] [INFO] Found 6/6 markers.
[2024-01-24 13:03:29,240] [INFO] Query marker FASTA was written to GCF_000732945.1_ASM73294v1_genomic.fna/markers.fasta
[2024-01-24 13:03:29,241] [INFO] Task started: Blastn
[2024-01-24 13:03:29,241] [INFO] Running command: blastn -query GCF_000732945.1_ASM73294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/reference_markers.fasta -out GCF_000732945.1_ASM73294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:30,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:30,180] [INFO] Selected 15 target genomes.
[2024-01-24 13:03:30,181] [INFO] Target genome list was writen to GCF_000732945.1_ASM73294v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:30,187] [INFO] Task started: fastANI
[2024-01-24 13:03:30,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg492c638e-8cd8-454d-b9bc-fb51b78ccdef/GCF_000732945.1_ASM73294v1_genomic.fna.gz --refList GCF_000732945.1_ASM73294v1_genomic.fna/target_genomes.txt --output GCF_000732945.1_ASM73294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:38,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:38,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:38,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:38,235] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:38,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:38,236] [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 atypicum	strain=R2070	GCA_000732945.1	191610	191610	type	True	100.0	779	786	95	conclusive
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	80.1513	459	786	95	below_threshold
Corynebacterium uberis	strain=18M0132	GCA_020616335.1	2883169	2883169	type	True	78.5361	241	786	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.3037	248	786	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.2408	241	786	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.1753	257	786	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000296405.1	29321	29321	type	True	78.0582	218	786	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000297795.2	29321	29321	type	True	78.0254	217	786	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	77.9007	203	786	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	77.8466	276	786	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.7994	235	786	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.6	261	786	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	77.1471	74	786	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	76.4284	131	786	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	76.2665	109	786	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:38,238] [INFO] DFAST Taxonomy check result was written to GCF_000732945.1_ASM73294v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:38,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:38,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:38,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/checkm_data
[2024-01-24 13:03:38,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:38,274] [INFO] Task started: CheckM
[2024-01-24 13:03:38,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000732945.1_ASM73294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000732945.1_ASM73294v1_genomic.fna/checkm_input GCF_000732945.1_ASM73294v1_genomic.fna/checkm_result
[2024-01-24 13:04:03,573] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:03,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:03,596] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:03,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:03,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000732945.1_ASM73294v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:03,597] [INFO] Task started: Blastn
[2024-01-24 13:04:03,598] [INFO] Running command: blastn -query GCF_000732945.1_ASM73294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ed24af-5c39-4b67-9f17-f9159c6634a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000732945.1_ASM73294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:05,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:05,003] [INFO] Selected 16 target genomes.
[2024-01-24 13:04:05,004] [INFO] Target genome list was writen to GCF_000732945.1_ASM73294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:05,016] [INFO] Task started: fastANI
[2024-01-24 13:04:05,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg492c638e-8cd8-454d-b9bc-fb51b78ccdef/GCF_000732945.1_ASM73294v1_genomic.fna.gz --refList GCF_000732945.1_ASM73294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000732945.1_ASM73294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:14,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:14,353] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:14,353] [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_000732945.1	s__Corynebacterium atypicum	100.0	781	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001941485.1	s__Corynebacterium frankenforstense	80.1219	461	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375365.1	s__Corynebacterium mastitidis	78.3037	248	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.261	184	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.1898	256	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000819445.1	s__Corynebacterium humireducens	78.1525	239	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000296405.1	s__Corynebacterium otitidis	78.0804	217	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.41	98.97	0.97	0.95	3	-
GCF_009734405.1	s__Corynebacterium sp009734405	77.877	208	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	77.8671	275	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017876455.1	s__Corynebacterium freneyi	77.6928	169	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCF_001056295.1	s__Corynebacterium halotolerans_A	77.5906	183	786	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	77.4553	204	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014490575.1	s__Corynebacterium sp014490575	77.1656	74	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_013450295.1	s__Streptomyces sp013450295	77.039	68	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	76.6179	133	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710915.1	s__Nocardia brasiliensis_A	76.0259	115	786	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:14,355] [INFO] GTDB search result was written to GCF_000732945.1_ASM73294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:14,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:14,359] [INFO] DFAST_QC result json was written to GCF_000732945.1_ASM73294v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:14,360] [INFO] DFAST_QC completed!
[2024-01-24 13:04:14,360] [INFO] Total running time: 0h0m54s