[2024-01-25 17:53:05,733] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference
[2024-01-25 17:53:06,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,894] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,894] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6c0d9a2-de0b-41be-9b3d-01550d08f7cc/GCF_002563965.1_ASM256396v1_genomic.fna.gz | prodigal -d GCF_002563965.1_ASM256396v1_genomic.fna/cds.fna -a GCF_002563965.1_ASM256396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:13,491] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:13,491] [INFO] Task started: HMMsearch
[2024-01-25 17:53:13,492] [INFO] Running command: hmmsearch --tblout GCF_002563965.1_ASM256396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/reference_markers.hmm GCF_002563965.1_ASM256396v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:13,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:13,688] [INFO] Found 6/6 markers.
[2024-01-25 17:53:13,709] [INFO] Query marker FASTA was written to GCF_002563965.1_ASM256396v1_genomic.fna/markers.fasta
[2024-01-25 17:53:13,709] [INFO] Task started: Blastn
[2024-01-25 17:53:13,710] [INFO] Running command: blastn -query GCF_002563965.1_ASM256396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/reference_markers.fasta -out GCF_002563965.1_ASM256396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:14,412] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:14,415] [INFO] Selected 18 target genomes.
[2024-01-25 17:53:14,415] [INFO] Target genome list was writen to GCF_002563965.1_ASM256396v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:14,442] [INFO] Task started: fastANI
[2024-01-25 17:53:14,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c0d9a2-de0b-41be-9b3d-01550d08f7cc/GCF_002563965.1_ASM256396v1_genomic.fna.gz --refList GCF_002563965.1_ASM256396v1_genomic.fna/target_genomes.txt --output GCF_002563965.1_ASM256396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:22,725] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:22,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:22,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:22,738] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:53:22,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:22,738] [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 renale	strain=DSM 20688	GCA_002563965.1	1724	1724	type	True	100.0	780	782	95	conclusive
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	99.9996	776	782	95	conclusive
Corynebacterium ulcerans	strain=FDAARGOS_1118	GCA_016727365.1	65058	65058	type	True	79.1748	75	782	95	below_threshold
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	78.7845	72	782	95	below_threshold
Corynebacterium callunae	strain=DSM 20147	GCA_000344785.1	1721	1721	type	True	78.4901	102	782	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.4704	157	782	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	78.259	134	782	95	below_threshold
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	78.2229	107	782	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	78.1344	133	782	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.0733	134	782	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.9839	190	782	95	below_threshold
Corynebacterium aquatimens	strain=DSM 45632	GCA_015752125.1	1190508	1190508	type	True	77.7627	95	782	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	77.7461	172	782	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	77.7201	150	782	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	77.6051	72	782	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	77.4789	101	782	95	below_threshold
Corynebacterium callunae	strain=DSM 20147	GCA_000420585.1	1721	1721	type	True	77.3764	95	782	95	below_threshold
Corynebacterium oculi	strain=NML 130210	GCA_001412105.1	1544416	1544416	type	True	76.986	111	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:22,749] [INFO] DFAST Taxonomy check result was written to GCF_002563965.1_ASM256396v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:22,750] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:22,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:22,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/checkm_data
[2024-01-25 17:53:22,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:22,777] [INFO] Task started: CheckM
[2024-01-25 17:53:22,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563965.1_ASM256396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563965.1_ASM256396v1_genomic.fna/checkm_input GCF_002563965.1_ASM256396v1_genomic.fna/checkm_result
[2024-01-25 17:53:45,472] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:45,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:45,491] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:45,492] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:45,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563965.1_ASM256396v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:45,492] [INFO] Task started: Blastn
[2024-01-25 17:53:45,492] [INFO] Running command: blastn -query GCF_002563965.1_ASM256396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb39af842-3e7a-45aa-9291-6c1a172ce34e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563965.1_ASM256396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:46,488] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:46,491] [INFO] Selected 21 target genomes.
[2024-01-25 17:53:46,491] [INFO] Target genome list was writen to GCF_002563965.1_ASM256396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:46,509] [INFO] Task started: fastANI
[2024-01-25 17:53:46,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c0d9a2-de0b-41be-9b3d-01550d08f7cc/GCF_002563965.1_ASM256396v1_genomic.fna.gz --refList GCF_002563965.1_ASM256396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563965.1_ASM256396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:56,080] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:56,092] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:56,092] [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_002563965.1	s__Corynebacterium renale	100.0	779	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	conclusive
GCF_900187135.1	s__Corynebacterium ulcerans	79.1299	71	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	-
GCF_002355155.1	s__Corynebacterium suranareeae	78.5274	110	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344785.1	s__Corynebacterium callunae	78.3932	100	782	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	78.3183	156	782	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	78.2337	163	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000478175.1	s__Corynebacterium sp000478175	78.1553	106	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_000835165.1	s__Corynebacterium marinum	78.0982	157	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.0588	191	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752125.1	s__Corynebacterium aquatimens	78.0385	97	782	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	77.9052	173	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000159135.1	s__Corynebacterium striatum	77.7466	126	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_004382825.2	s__Corynebacterium silvaticum	77.6968	70	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_000159115.1	s__Corynebacterium accolens	77.4789	101	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.20	96.99	0.95	0.94	10	-
GCF_001806875.1	s__Corynebacterium sp001806875	77.4737	90	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900618065.1	s__Corynebacterium sp900618065	77.4491	118	782	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	77.4425	134	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_000379425.1	s__Corynebacterium lubricantis	77.2278	115	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412105.1	s__Corynebacterium oculi	77.0094	110	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	76.9595	123	782	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114925.1	s__Corynebacterium faecipullorum	76.265	84	782	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 17:53:56,094] [INFO] GTDB search result was written to GCF_002563965.1_ASM256396v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:56,095] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:56,099] [INFO] DFAST_QC result json was written to GCF_002563965.1_ASM256396v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:56,099] [INFO] DFAST_QC completed!
[2024-01-25 17:53:56,100] [INFO] Total running time: 0h0m50s