[2024-01-24 12:31:34,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference
[2024-01-24 12:31:35,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,425] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dde62b0-bfa5-4de7-85b0-a6fca3b92c79/GCF_000688415.1_ASM68841v1_genomic.fna.gz | prodigal -d GCF_000688415.1_ASM68841v1_genomic.fna/cds.fna -a GCF_000688415.1_ASM68841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:42,467] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:42,468] [INFO] Task started: HMMsearch
[2024-01-24 12:31:42,468] [INFO] Running command: hmmsearch --tblout GCF_000688415.1_ASM68841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/reference_markers.hmm GCF_000688415.1_ASM68841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:42,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:42,684] [INFO] Found 6/6 markers.
[2024-01-24 12:31:42,708] [INFO] Query marker FASTA was written to GCF_000688415.1_ASM68841v1_genomic.fna/markers.fasta
[2024-01-24 12:31:42,709] [INFO] Task started: Blastn
[2024-01-24 12:31:42,709] [INFO] Running command: blastn -query GCF_000688415.1_ASM68841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/reference_markers.fasta -out GCF_000688415.1_ASM68841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:43,512] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:43,517] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:43,517] [INFO] Target genome list was writen to GCF_000688415.1_ASM68841v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:43,520] [INFO] Task started: fastANI
[2024-01-24 12:31:43,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde62b0-bfa5-4de7-85b0-a6fca3b92c79/GCF_000688415.1_ASM68841v1_genomic.fna.gz --refList GCF_000688415.1_ASM68841v1_genomic.fna/target_genomes.txt --output GCF_000688415.1_ASM68841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:48,844] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:48,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:48,864] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:48,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:48,865] [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 pseudodiphtheriticum	strain=DSM 44287	GCA_000688415.1	37637	37637	type	True	100.0	746	746	95	conclusive
Corynebacterium propinquum	strain=DSM 44285	GCA_000375525.1	43769	43769	type	True	86.0582	567	746	95	below_threshold
Corynebacterium propinquum	strain=FDAARGOS_1112	GCA_016728665.1	43769	43769	type	True	85.9763	582	746	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.1535	90	746	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	78.1083	88	746	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.0814	70	746	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.0422	89	746	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306 = 9.6	GCA_001941425.1	1697	1697	type	True	77.9396	72	746	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	77.8049	51	746	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306	GCA_000164115.1	1697	1697	type	True	77.7965	70	746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,867] [INFO] DFAST Taxonomy check result was written to GCF_000688415.1_ASM68841v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:48,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:48,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:48,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/checkm_data
[2024-01-24 12:31:48,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:48,898] [INFO] Task started: CheckM
[2024-01-24 12:31:48,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000688415.1_ASM68841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000688415.1_ASM68841v1_genomic.fna/checkm_input GCF_000688415.1_ASM68841v1_genomic.fna/checkm_result
[2024-01-24 12:32:14,438] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:14,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:14,463] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:14,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:14,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000688415.1_ASM68841v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:14,464] [INFO] Task started: Blastn
[2024-01-24 12:32:14,465] [INFO] Running command: blastn -query GCF_000688415.1_ASM68841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54785301-8e22-4662-9eb4-699ab1eab314/dqc_reference/reference_markers_gtdb.fasta -out GCF_000688415.1_ASM68841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:15,603] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:15,607] [INFO] Selected 15 target genomes.
[2024-01-24 12:32:15,607] [INFO] Target genome list was writen to GCF_000688415.1_ASM68841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:15,620] [INFO] Task started: fastANI
[2024-01-24 12:32:15,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dde62b0-bfa5-4de7-85b0-a6fca3b92c79/GCF_000688415.1_ASM68841v1_genomic.fna.gz --refList GCF_000688415.1_ASM68841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000688415.1_ASM68841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:22,342] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:22,366] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:22,367] [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_000688415.1	s__Corynebacterium pseudodiphtheriticum	100.0	746	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.46	98.41	0.95	0.91	10	conclusive
GCF_000375525.1	s__Corynebacterium propinquum	86.0448	568	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.98	97.48	0.95	0.92	13	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.0834	88	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000420605.1	s__Corynebacterium massiliense	78.0815	70	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	78.0617	70	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_001941425.1	s__Corynebacterium ammoniagenes	77.9396	72	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	98.81	0.99	0.95	5	-
GCF_001815935.1	s__Corynebacterium sp001815935	77.8871	93	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539985.1	s__Corynebacterium sp900539985	77.7436	70	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_001812805.1	s__Corynebacterium sp001812805	77.7056	70	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	77.5414	64	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	77.5213	67	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	77.44	82	746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCA_900618065.1	s__Corynebacterium sp900618065	77.0752	66	746	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 12:32:22,369] [INFO] GTDB search result was written to GCF_000688415.1_ASM68841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:22,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:22,373] [INFO] DFAST_QC result json was written to GCF_000688415.1_ASM68841v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:22,373] [INFO] DFAST_QC completed!
[2024-01-24 12:32:22,373] [INFO] Total running time: 0h0m48s