[2024-01-25 18:57:05,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:05,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:05,764] [INFO] DQC Reference Directory: /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference
[2024-01-25 18:57:06,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:06,892] [INFO] Task started: Prodigal
[2024-01-25 18:57:06,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b9833bb-ce49-4b8b-8194-3362756399bf/GCF_020616335.1_ASM2061633v1_genomic.fna.gz | prodigal -d GCF_020616335.1_ASM2061633v1_genomic.fna/cds.fna -a GCF_020616335.1_ASM2061633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:14,276] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:14,276] [INFO] Task started: HMMsearch
[2024-01-25 18:57:14,276] [INFO] Running command: hmmsearch --tblout GCF_020616335.1_ASM2061633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/reference_markers.hmm GCF_020616335.1_ASM2061633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:14,453] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:14,454] [INFO] Found 6/6 markers.
[2024-01-25 18:57:14,477] [INFO] Query marker FASTA was written to GCF_020616335.1_ASM2061633v1_genomic.fna/markers.fasta
[2024-01-25 18:57:14,478] [INFO] Task started: Blastn
[2024-01-25 18:57:14,478] [INFO] Running command: blastn -query GCF_020616335.1_ASM2061633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/reference_markers.fasta -out GCF_020616335.1_ASM2061633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:15,374] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:15,377] [INFO] Selected 13 target genomes.
[2024-01-25 18:57:15,377] [INFO] Target genome list was writen to GCF_020616335.1_ASM2061633v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:15,389] [INFO] Task started: fastANI
[2024-01-25 18:57:15,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9833bb-ce49-4b8b-8194-3362756399bf/GCF_020616335.1_ASM2061633v1_genomic.fna.gz --refList GCF_020616335.1_ASM2061633v1_genomic.fna/target_genomes.txt --output GCF_020616335.1_ASM2061633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:21,816] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:21,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:21,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:21,825] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:21,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:21,826] [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 uberis	strain=18M0132	GCA_020616335.1	2883169	2883169	type	True	100.0	843	844	95	conclusive
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	79.4004	359	844	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	79.2659	345	844	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.9546	297	844	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.9154	249	844	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.6094	290	844	95	below_threshold
Corynebacterium oculi	strain=NML 130210	GCA_001412105.1	1544416	1544416	type	True	78.5504	303	844	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	78.3941	278	844	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	78.3391	199	844	95	below_threshold
Corynebacterium atypicum	strain=R2070	GCA_000732945.1	191610	191610	type	True	78.3167	234	844	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.2612	250	844	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000296405.1	29321	29321	type	True	78.1542	186	844	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000297795.2	29321	29321	type	True	78.0154	187	844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:21,831] [INFO] DFAST Taxonomy check result was written to GCF_020616335.1_ASM2061633v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:21,831] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:21,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:21,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/checkm_data
[2024-01-25 18:57:21,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:21,868] [INFO] Task started: CheckM
[2024-01-25 18:57:21,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020616335.1_ASM2061633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020616335.1_ASM2061633v1_genomic.fna/checkm_input GCF_020616335.1_ASM2061633v1_genomic.fna/checkm_result
[2024-01-25 18:57:46,412] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:46,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:46,432] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:46,433] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:46,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020616335.1_ASM2061633v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:46,433] [INFO] Task started: Blastn
[2024-01-25 18:57:46,433] [INFO] Running command: blastn -query GCF_020616335.1_ASM2061633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d754b1-329e-4a11-a119-d17ca0a89098/dqc_reference/reference_markers_gtdb.fasta -out GCF_020616335.1_ASM2061633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:47,761] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:47,763] [INFO] Selected 15 target genomes.
[2024-01-25 18:57:47,764] [INFO] Target genome list was writen to GCF_020616335.1_ASM2061633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:47,783] [INFO] Task started: fastANI
[2024-01-25 18:57:47,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b9833bb-ce49-4b8b-8194-3362756399bf/GCF_020616335.1_ASM2061633v1_genomic.fna.gz --refList GCF_020616335.1_ASM2061633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020616335.1_ASM2061633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:55,057] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:55,067] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:55,067] [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_000375365.1	s__Corynebacterium mastitidis	79.3729	361	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	79.199	343	844	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	78.9893	298	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000835165.1	s__Corynebacterium marinum	78.7926	256	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.7875	245	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.6283	216	844	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	78.6194	281	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.589	256	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_001412105.1	s__Corynebacterium oculi	78.5504	303	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412085.1	s__Corynebacterium lowii	78.3798	279	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	78.3299	196	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732945.1	s__Corynebacterium atypicum	78.2973	232	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	78.2251	224	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000296405.1	s__Corynebacterium otitidis	78.1741	185	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.41	98.97	0.97	0.95	3	-
GCF_003955685.1	s__Corynebacterium sp003955685	78.1499	243	844	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:55,068] [INFO] GTDB search result was written to GCF_020616335.1_ASM2061633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:55,068] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:55,071] [INFO] DFAST_QC result json was written to GCF_020616335.1_ASM2061633v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:55,072] [INFO] DFAST_QC completed!
[2024-01-25 18:57:55,072] [INFO] Total running time: 0h0m49s