[2024-01-24 14:47:55,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference
[2024-01-24 14:47:58,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,526] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eb5ce64-392c-452e-a7ae-aa08aff9d07c/GCF_016889425.1_ASM1688942v1_genomic.fna.gz | prodigal -d GCF_016889425.1_ASM1688942v1_genomic.fna/cds.fna -a GCF_016889425.1_ASM1688942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:06,863] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:06,864] [INFO] Task started: HMMsearch
[2024-01-24 14:48:06,864] [INFO] Running command: hmmsearch --tblout GCF_016889425.1_ASM1688942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/reference_markers.hmm GCF_016889425.1_ASM1688942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:07,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:07,152] [INFO] Found 6/6 markers.
[2024-01-24 14:48:07,176] [INFO] Query marker FASTA was written to GCF_016889425.1_ASM1688942v1_genomic.fna/markers.fasta
[2024-01-24 14:48:07,177] [INFO] Task started: Blastn
[2024-01-24 14:48:07,177] [INFO] Running command: blastn -query GCF_016889425.1_ASM1688942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/reference_markers.fasta -out GCF_016889425.1_ASM1688942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:08,109] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:08,113] [INFO] Selected 10 target genomes.
[2024-01-24 14:48:08,113] [INFO] Target genome list was writen to GCF_016889425.1_ASM1688942v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:08,117] [INFO] Task started: fastANI
[2024-01-24 14:48:08,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb5ce64-392c-452e-a7ae-aa08aff9d07c/GCF_016889425.1_ASM1688942v1_genomic.fna.gz --refList GCF_016889425.1_ASM1688942v1_genomic.fna/target_genomes.txt --output GCF_016889425.1_ASM1688942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:15,676] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:15,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:15,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:15,686] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:48:15,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:15,686] [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 amycolatum	strain=FDAARGOS_1189	GCA_016889425.1	43765	43765	type	True	100.0	821	824	95	conclusive
Corynebacterium amycolatum	strain=LK23	GCA_014335175.1	43765	43765	type	True	99.9915	812	824	95	conclusive
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	80.2298	410	824	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	79.2039	238	824	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	79.0735	242	824	95	below_threshold
Corynebacterium xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	78.3059	257	824	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	78.0926	151	824	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	77.475	62	824	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	76.0279	60	824	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:15,694] [INFO] DFAST Taxonomy check result was written to GCF_016889425.1_ASM1688942v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:15,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:15,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:15,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/checkm_data
[2024-01-24 14:48:15,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:15,724] [INFO] Task started: CheckM
[2024-01-24 14:48:15,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016889425.1_ASM1688942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016889425.1_ASM1688942v1_genomic.fna/checkm_input GCF_016889425.1_ASM1688942v1_genomic.fna/checkm_result
[2024-01-24 14:48:46,161] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:46,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:46,181] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:46,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:46,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016889425.1_ASM1688942v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:46,182] [INFO] Task started: Blastn
[2024-01-24 14:48:46,182] [INFO] Running command: blastn -query GCF_016889425.1_ASM1688942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a41e0e-17b9-40b3-a747-5c06ac86e9f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016889425.1_ASM1688942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:47,625] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:47,632] [INFO] Selected 8 target genomes.
[2024-01-24 14:48:47,632] [INFO] Target genome list was writen to GCF_016889425.1_ASM1688942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:47,639] [INFO] Task started: fastANI
[2024-01-24 14:48:47,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb5ce64-392c-452e-a7ae-aa08aff9d07c/GCF_016889425.1_ASM1688942v1_genomic.fna.gz --refList GCF_016889425.1_ASM1688942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016889425.1_ASM1688942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:52,463] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:52,474] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:52,474] [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_016889425.1	s__Corynebacterium amycolatum	100.0	823	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.33	95.20	0.94	0.89	32	conclusive
GCF_000173655.1	s__Corynebacterium amycolatum_A	94.5395	753	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.32	95.17	0.90	0.87	42	-
GCF_001054325.1	s__Corynebacterium vitaeruminis_A	92.3002	741	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900519355.1	s__Corynebacterium lactis_A	80.2886	428	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274895.1	s__Corynebacterium lactis	80.2233	410	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876455.1	s__Corynebacterium freneyi	79.2076	239	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCF_017942225.1	s__Corynebacterium sp017942225	78.2932	98	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838715.1	s__Corynebacterium sp012838715	77.9538	178	824	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:52,475] [INFO] GTDB search result was written to GCF_016889425.1_ASM1688942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:52,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:52,479] [INFO] DFAST_QC result json was written to GCF_016889425.1_ASM1688942v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:52,479] [INFO] DFAST_QC completed!
[2024-01-24 14:48:52,479] [INFO] Total running time: 0h0m57s