[2024-01-24 12:47:13,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:13,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:13,985] [INFO] DQC Reference Directory: /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference
[2024-01-24 12:47:15,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,418] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgff952905-85cb-4d58-9268-b8a3875924da/GCF_000297795.2_ASM29779v2_genomic.fna.gz | prodigal -d GCF_000297795.2_ASM29779v2_genomic.fna/cds.fna -a GCF_000297795.2_ASM29779v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:20,810] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:20,811] [INFO] Task started: HMMsearch
[2024-01-24 12:47:20,811] [INFO] Running command: hmmsearch --tblout GCF_000297795.2_ASM29779v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/reference_markers.hmm GCF_000297795.2_ASM29779v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:21,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:21,081] [INFO] Found 6/6 markers.
[2024-01-24 12:47:21,113] [INFO] Query marker FASTA was written to GCF_000297795.2_ASM29779v2_genomic.fna/markers.fasta
[2024-01-24 12:47:21,113] [INFO] Task started: Blastn
[2024-01-24 12:47:21,114] [INFO] Running command: blastn -query GCF_000297795.2_ASM29779v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/reference_markers.fasta -out GCF_000297795.2_ASM29779v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:22,394] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:22,397] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:22,398] [INFO] Target genome list was writen to GCF_000297795.2_ASM29779v2_genomic.fna/target_genomes.txt
[2024-01-24 12:47:22,403] [INFO] Task started: fastANI
[2024-01-24 12:47:22,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgff952905-85cb-4d58-9268-b8a3875924da/GCF_000297795.2_ASM29779v2_genomic.fna.gz --refList GCF_000297795.2_ASM29779v2_genomic.fna/target_genomes.txt --output GCF_000297795.2_ASM29779v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:30,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:30,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:30,408] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:30,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:30,409] [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 otitidis	strain=ATCC 51513	GCA_000297795.2	29321	29321	type	True	99.9995	709	712	95	conclusive
Corynebacterium otitidis	strain=ATCC 51513	GCA_000296405.1	29321	29321	type	True	99.8398	698	712	95	conclusive
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	79.6673	418	712	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.9424	344	712	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.8992	342	712	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.7707	306	712	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	78.6839	280	712	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.6648	320	712	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.4493	316	712	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.4464	327	712	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.3857	300	712	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.1479	212	712	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	75.8118	249	712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,411] [INFO] DFAST Taxonomy check result was written to GCF_000297795.2_ASM29779v2_genomic.fna/tc_result.tsv
[2024-01-24 12:47:30,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:30,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:30,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/checkm_data
[2024-01-24 12:47:30,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:30,440] [INFO] Task started: CheckM
[2024-01-24 12:47:30,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000297795.2_ASM29779v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000297795.2_ASM29779v2_genomic.fna/checkm_input GCF_000297795.2_ASM29779v2_genomic.fna/checkm_result
[2024-01-24 12:47:51,795] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:51,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:51,810] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:51,811] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:51,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000297795.2_ASM29779v2_genomic.fna/markers.fasta)
[2024-01-24 12:47:51,811] [INFO] Task started: Blastn
[2024-01-24 12:47:51,811] [INFO] Running command: blastn -query GCF_000297795.2_ASM29779v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga6dc3175-8a74-48ec-afe3-6936ed67d6e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000297795.2_ASM29779v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:53,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:53,588] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:53,588] [INFO] Target genome list was writen to GCF_000297795.2_ASM29779v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:53,597] [INFO] Task started: fastANI
[2024-01-24 12:47:53,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgff952905-85cb-4d58-9268-b8a3875924da/GCF_000297795.2_ASM29779v2_genomic.fna.gz --refList GCF_000297795.2_ASM29779v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000297795.2_ASM29779v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:02,336] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:02,356] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:02,357] [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_000296405.1	s__Corynebacterium otitidis	99.8398	698	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.41	98.97	0.97	0.95	3	conclusive
GCF_001941485.1	s__Corynebacterium frankenforstense	79.711	415	712	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	78.9561	343	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.7499	308	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000577555.1	s__Corynebacterium jeddahense	78.6683	281	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.6634	320	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.4341	328	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000375365.1	s__Corynebacterium mastitidis	78.3312	303	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	78.1598	259	712	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	78.0105	204	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001482365.1	s__Kocuria flava	76.3731	219	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_004005495.1	s__Streptomyces sp004005495	75.8226	227	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718635.1	s__Streptomyces varsoviensis	75.7346	242	712	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,359] [INFO] GTDB search result was written to GCF_000297795.2_ASM29779v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:02,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:02,366] [INFO] DFAST_QC result json was written to GCF_000297795.2_ASM29779v2_genomic.fna/dqc_result.json
[2024-01-24 12:48:02,366] [INFO] DFAST_QC completed!
[2024-01-24 12:48:02,367] [INFO] Total running time: 0h0m48s