[2024-01-25 17:47:05,692] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:05,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:05,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference
[2024-01-25 17:47:06,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:06,831] [INFO] Task started: Prodigal
[2024-01-25 17:47:06,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba9f924-7f94-4298-b281-e8e25be5e537/GCF_016727365.1_ASM1672736v1_genomic.fna.gz | prodigal -d GCF_016727365.1_ASM1672736v1_genomic.fna/cds.fna -a GCF_016727365.1_ASM1672736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:13,375] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:13,375] [INFO] Task started: HMMsearch
[2024-01-25 17:47:13,375] [INFO] Running command: hmmsearch --tblout GCF_016727365.1_ASM1672736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/reference_markers.hmm GCF_016727365.1_ASM1672736v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:13,562] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:13,563] [INFO] Found 6/6 markers.
[2024-01-25 17:47:13,585] [INFO] Query marker FASTA was written to GCF_016727365.1_ASM1672736v1_genomic.fna/markers.fasta
[2024-01-25 17:47:13,585] [INFO] Task started: Blastn
[2024-01-25 17:47:13,586] [INFO] Running command: blastn -query GCF_016727365.1_ASM1672736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/reference_markers.fasta -out GCF_016727365.1_ASM1672736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:14,241] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:14,243] [INFO] Selected 7 target genomes.
[2024-01-25 17:47:14,244] [INFO] Target genome list was writen to GCF_016727365.1_ASM1672736v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:14,254] [INFO] Task started: fastANI
[2024-01-25 17:47:14,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba9f924-7f94-4298-b281-e8e25be5e537/GCF_016727365.1_ASM1672736v1_genomic.fna.gz --refList GCF_016727365.1_ASM1672736v1_genomic.fna/target_genomes.txt --output GCF_016727365.1_ASM1672736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:18,296] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:18,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:18,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:18,303] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:47:18,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:18,303] [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 ulcerans	strain=FDAARGOS_1118	GCA_016727365.1	65058	65058	type	True	100.0	816	817	95	conclusive
Corynebacterium ulcerans	strain=NCTC7910	GCA_900187135.1	65058	65058	type	True	99.9948	815	817	95	conclusive
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	91.0549	744	817	95	below_threshold
Corynebacterium pseudotuberculosis	strain=ATCC 19410	GCA_002155265.1	1719	1719	type	True	85.0712	692	817	95	below_threshold
Corynebacterium pseudotuberculosis	strain=DSM 20689	GCA_003634885.1	1719	1719	type	True	85.0249	724	817	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	78.7193	78	817	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.4617	81	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:18,304] [INFO] DFAST Taxonomy check result was written to GCF_016727365.1_ASM1672736v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:18,305] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:18,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:18,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/checkm_data
[2024-01-25 17:47:18,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:18,333] [INFO] Task started: CheckM
[2024-01-25 17:47:18,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016727365.1_ASM1672736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016727365.1_ASM1672736v1_genomic.fna/checkm_input GCF_016727365.1_ASM1672736v1_genomic.fna/checkm_result
[2024-01-25 17:47:41,156] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:41,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:41,180] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:41,180] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:41,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016727365.1_ASM1672736v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:41,180] [INFO] Task started: Blastn
[2024-01-25 17:47:41,180] [INFO] Running command: blastn -query GCF_016727365.1_ASM1672736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebc25da4-afce-4f4f-a876-91008e00e8a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016727365.1_ASM1672736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:42,226] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:42,229] [INFO] Selected 12 target genomes.
[2024-01-25 17:47:42,229] [INFO] Target genome list was writen to GCF_016727365.1_ASM1672736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:42,240] [INFO] Task started: fastANI
[2024-01-25 17:47:42,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba9f924-7f94-4298-b281-e8e25be5e537/GCF_016727365.1_ASM1672736v1_genomic.fna.gz --refList GCF_016727365.1_ASM1672736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016727365.1_ASM1672736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:48,701] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:48,708] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:48,709] [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_900187135.1	s__Corynebacterium ulcerans	99.9948	815	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.24	95.82	0.97	0.95	38	conclusive
GCF_004382825.2	s__Corynebacterium silvaticum	91.0549	744	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_002155265.1	s__Corynebacterium pseudotuberculosis	85.064	692	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.58	98.61	0.99	0.97	131	-
GCF_001457455.1	s__Corynebacterium diphtheriae	80.0134	156	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_902702935.1	s__Corynebacterium rouxii	79.9724	165	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	79.2784	79	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643015.1	s__Corynebacterium crudilactis	78.9866	79	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563965.1	s__Corynebacterium renale	78.9098	74	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
GCF_000344785.1	s__Corynebacterium callunae	78.5336	98	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734385.1	s__Corynebacterium sp009734385	78.2963	91	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372385.1	s__Corynebacterium ciconiae	77.4617	81	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806875.1	s__Corynebacterium sp001806875	77.129	61	817	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 17:47:48,710] [INFO] GTDB search result was written to GCF_016727365.1_ASM1672736v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:48,710] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:48,713] [INFO] DFAST_QC result json was written to GCF_016727365.1_ASM1672736v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:48,713] [INFO] DFAST_QC completed!
[2024-01-25 17:47:48,713] [INFO] Total running time: 0h0m43s