[2024-01-24 12:30:51,240] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:51,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:51,242] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference
[2024-01-24 12:30:52,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:52,557] [INFO] Task started: Prodigal
[2024-01-24 12:30:52,557] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7392f5e-5fd4-4325-8290-079a938c62fe/GCF_003285565.1_ASM328556v1_genomic.fna.gz | prodigal -d GCF_003285565.1_ASM328556v1_genomic.fna/cds.fna -a GCF_003285565.1_ASM328556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:59,202] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:59,203] [INFO] Task started: HMMsearch
[2024-01-24 12:30:59,203] [INFO] Running command: hmmsearch --tblout GCF_003285565.1_ASM328556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/reference_markers.hmm GCF_003285565.1_ASM328556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:59,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:59,422] [INFO] Found 6/6 markers.
[2024-01-24 12:30:59,448] [INFO] Query marker FASTA was written to GCF_003285565.1_ASM328556v1_genomic.fna/markers.fasta
[2024-01-24 12:30:59,449] [INFO] Task started: Blastn
[2024-01-24 12:30:59,449] [INFO] Running command: blastn -query GCF_003285565.1_ASM328556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/reference_markers.fasta -out GCF_003285565.1_ASM328556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:00,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:00,360] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:00,361] [INFO] Target genome list was writen to GCF_003285565.1_ASM328556v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:00,409] [INFO] Task started: fastANI
[2024-01-24 12:31:00,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7392f5e-5fd4-4325-8290-079a938c62fe/GCF_003285565.1_ASM328556v1_genomic.fna.gz --refList GCF_003285565.1_ASM328556v1_genomic.fna/target_genomes.txt --output GCF_003285565.1_ASM328556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:08,109] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:08,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:08,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:08,127] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:08,127] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:08,127] [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 heidelbergense	strain=DSM 104638	GCA_003285565.1	2055947	2055947	type	True	100.0	675	685	95	conclusive
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	78.1903	191	685	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.1818	197	685	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	78.0962	197	685	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	78.0931	187	685	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	78.0101	215	685	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	78.0009	199	685	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	77.9934	213	685	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	77.9777	192	685	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	77.9626	197	685	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	77.8846	150	685	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	77.8727	156	685	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000296405.1	29321	29321	type	True	77.3975	101	685	95	below_threshold
Corynebacterium otitidis	strain=ATCC 51513	GCA_000297795.2	29321	29321	type	True	77.3104	104	685	95	below_threshold
Amycolatopsis jiangsuensis	strain=DSM 45859	GCA_014204865.1	1181879	1181879	type	True	76.3764	69	685	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	76.2049	67	685	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:08,129] [INFO] DFAST Taxonomy check result was written to GCF_003285565.1_ASM328556v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:08,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:08,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:08,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/checkm_data
[2024-01-24 12:31:08,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:08,155] [INFO] Task started: CheckM
[2024-01-24 12:31:08,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003285565.1_ASM328556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003285565.1_ASM328556v1_genomic.fna/checkm_input GCF_003285565.1_ASM328556v1_genomic.fna/checkm_result
[2024-01-24 12:31:33,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:33,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:33,072] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:33,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:33,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003285565.1_ASM328556v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:33,074] [INFO] Task started: Blastn
[2024-01-24 12:31:33,074] [INFO] Running command: blastn -query GCF_003285565.1_ASM328556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf5b38fe-deb4-4f2e-b3e4-d1efacf30cc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003285565.1_ASM328556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:34,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:34,381] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:34,382] [INFO] Target genome list was writen to GCF_003285565.1_ASM328556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:34,401] [INFO] Task started: fastANI
[2024-01-24 12:31:34,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7392f5e-5fd4-4325-8290-079a938c62fe/GCF_003285565.1_ASM328556v1_genomic.fna.gz --refList GCF_003285565.1_ASM328556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003285565.1_ASM328556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:43,686] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:43,704] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:43,704] [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_003285565.1	s__Corynebacterium heidelbergense	100.0	675	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	conclusive
GCF_000738265.1	s__Corynebacterium jeikeium_A	78.4642	205	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCA_019114175.1	s__Corynebacterium gallistercoris	78.3075	186	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.2218	214	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163435.1	s__Corynebacterium jeikeium	78.1818	197	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_001815985.1	s__Corynebacterium sp001815985	78.1739	195	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_001807485.1	s__Corynebacterium sp001807485	78.1116	219	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000183325.1	s__Corynebacterium bovis	78.1	186	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCF_001054945.1	s__Corynebacterium falsenii_A	78.0504	160	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.0009	199	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCA_019120635.1	s__Corynebacterium intestinavium	77.8993	187	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351405.1	s__Corynebacterium sp015351405	77.8788	155	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	77.4443	158	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_001941505.1	s__Corynebacterium sphenisci	77.4359	190	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296405.1	s__Corynebacterium otitidis	77.3975	101	685	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.41	98.97	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,708] [INFO] GTDB search result was written to GCF_003285565.1_ASM328556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:43,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:43,713] [INFO] DFAST_QC result json was written to GCF_003285565.1_ASM328556v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:43,713] [INFO] DFAST_QC completed!
[2024-01-24 12:31:43,713] [INFO] Total running time: 0h0m52s