[2024-01-25 18:14:06,209] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:06,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:06,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference
[2024-01-25 18:14:07,333] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:07,333] [INFO] Task started: Prodigal
[2024-01-25 18:14:07,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg047e5b61-1c80-493c-adac-4694ff08180a/GCF_016403285.1_ASM1640328v1_genomic.fna.gz | prodigal -d GCF_016403285.1_ASM1640328v1_genomic.fna/cds.fna -a GCF_016403285.1_ASM1640328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:15,898] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:15,899] [INFO] Task started: HMMsearch
[2024-01-25 18:14:15,899] [INFO] Running command: hmmsearch --tblout GCF_016403285.1_ASM1640328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/reference_markers.hmm GCF_016403285.1_ASM1640328v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:16,094] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:16,096] [INFO] Found 6/6 markers.
[2024-01-25 18:14:16,121] [INFO] Query marker FASTA was written to GCF_016403285.1_ASM1640328v1_genomic.fna/markers.fasta
[2024-01-25 18:14:16,121] [INFO] Task started: Blastn
[2024-01-25 18:14:16,121] [INFO] Running command: blastn -query GCF_016403285.1_ASM1640328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/reference_markers.fasta -out GCF_016403285.1_ASM1640328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:16,880] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:16,882] [INFO] Selected 9 target genomes.
[2024-01-25 18:14:16,882] [INFO] Target genome list was writen to GCF_016403285.1_ASM1640328v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:16,891] [INFO] Task started: fastANI
[2024-01-25 18:14:16,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg047e5b61-1c80-493c-adac-4694ff08180a/GCF_016403285.1_ASM1640328v1_genomic.fna.gz --refList GCF_016403285.1_ASM1640328v1_genomic.fna/target_genomes.txt --output GCF_016403285.1_ASM1640328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:25,064] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:25,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:25,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:25,072] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:14:25,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:25,072] [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 striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	100.0	983	984	95	conclusive
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	99.9859	968	984	95	conclusive
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	99.9514	955	984	95	conclusive
Corynebacterium striatum	strain=ATCC 6940	GCA_000159135.1	43770	43770	type	True	99.7792	912	984	95	conclusive
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	80.9676	396	984	95	below_threshold
Corynebacterium minutissimum	strain=NCTC10288	GCA_900478045.1	38301	38301	type	True	80.5645	404	984	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	80.3748	334	984	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.7643	332	984	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	78.1071	132	984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:25,074] [INFO] DFAST Taxonomy check result was written to GCF_016403285.1_ASM1640328v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:25,074] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:25,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:25,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/checkm_data
[2024-01-25 18:14:25,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:25,126] [INFO] Task started: CheckM
[2024-01-25 18:14:25,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016403285.1_ASM1640328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016403285.1_ASM1640328v1_genomic.fna/checkm_input GCF_016403285.1_ASM1640328v1_genomic.fna/checkm_result
[2024-01-25 18:14:53,352] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:53,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:53,384] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:53,384] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:53,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016403285.1_ASM1640328v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:53,384] [INFO] Task started: Blastn
[2024-01-25 18:14:53,384] [INFO] Running command: blastn -query GCF_016403285.1_ASM1640328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4404c6-0f24-42a0-b684-5d4ee7b835fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016403285.1_ASM1640328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:54,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:54,512] [INFO] Selected 15 target genomes.
[2024-01-25 18:14:54,512] [INFO] Target genome list was writen to GCF_016403285.1_ASM1640328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:54,533] [INFO] Task started: fastANI
[2024-01-25 18:14:54,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg047e5b61-1c80-493c-adac-4694ff08180a/GCF_016403285.1_ASM1640328v1_genomic.fna.gz --refList GCF_016403285.1_ASM1640328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016403285.1_ASM1640328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:02,833] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:02,844] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:02,844] [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_000159135.1	s__Corynebacterium striatum	99.7559	913	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	conclusive
GCF_001586215.1	s__Corynebacterium simulans	86.6133	653	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_900092335.1	s__Corynebacterium phoceense	80.9438	392	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	80.8329	393	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	80.6563	420	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_001836165.1	s__Corynebacterium sp001836165	80.4244	424	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_016728705.1	s__Corynebacterium sp001807205	80.406	428	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	80.3778	352	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCF_000805675.1	s__Corynebacterium minutissimum	80.367	392	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	6	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	80.2961	336	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	79.8575	327	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_000980815.1	s__Corynebacterium camporealensis	79.7479	329	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCA_900539985.1	s__Corynebacterium sp900539985	79.621	309	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_001815935.1	s__Corynebacterium sp001815935	79.3592	328	984	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	78.1264	132	984	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:02,845] [INFO] GTDB search result was written to GCF_016403285.1_ASM1640328v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:02,846] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:02,849] [INFO] DFAST_QC result json was written to GCF_016403285.1_ASM1640328v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:02,849] [INFO] DFAST_QC completed!
[2024-01-25 18:15:02,849] [INFO] Total running time: 0h0m57s