[2024-01-24 13:55:25,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference
[2024-01-24 13:55:26,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,624] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,624] [INFO] Running command: gunzip -c /var/lib/cwl/stgefc60f1b-37af-4b86-8767-e364246a0af6/GCF_014262665.1_ASM1426266v1_genomic.fna.gz | prodigal -d GCF_014262665.1_ASM1426266v1_genomic.fna/cds.fna -a GCF_014262665.1_ASM1426266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:34,079] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:34,080] [INFO] Task started: HMMsearch
[2024-01-24 13:55:34,080] [INFO] Running command: hmmsearch --tblout GCF_014262665.1_ASM1426266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/reference_markers.hmm GCF_014262665.1_ASM1426266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:34,294] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:34,295] [INFO] Found 6/6 markers.
[2024-01-24 13:55:34,317] [INFO] Query marker FASTA was written to GCF_014262665.1_ASM1426266v1_genomic.fna/markers.fasta
[2024-01-24 13:55:34,317] [INFO] Task started: Blastn
[2024-01-24 13:55:34,317] [INFO] Running command: blastn -query GCF_014262665.1_ASM1426266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/reference_markers.fasta -out GCF_014262665.1_ASM1426266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,980] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,983] [INFO] Selected 19 target genomes.
[2024-01-24 13:55:34,984] [INFO] Target genome list was writen to GCF_014262665.1_ASM1426266v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:35,010] [INFO] Task started: fastANI
[2024-01-24 13:55:35,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc60f1b-37af-4b86-8767-e364246a0af6/GCF_014262665.1_ASM1426266v1_genomic.fna.gz --refList GCF_014262665.1_ASM1426266v1_genomic.fna/target_genomes.txt --output GCF_014262665.1_ASM1426266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:46,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:46,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:46,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:46,039] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:46,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:46,039] [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 anserum	strain=23H37-10	GCA_014262665.1	2684406	2684406	type	True	100.0	735	736	95	conclusive
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.1108	225	736	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	78.9668	108	736	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.7455	97	736	95	below_threshold
Corynebacterium auriscanis	strain=CIP 106629	GCA_000767255.1	99807	99807	type	True	78.5875	92	736	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	78.213	145	736	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	78.0941	139	736	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.0589	53	736	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	77.837	52	736	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	77.4114	51	736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:46,041] [INFO] DFAST Taxonomy check result was written to GCF_014262665.1_ASM1426266v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:46,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:46,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:46,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/checkm_data
[2024-01-24 13:55:46,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:46,073] [INFO] Task started: CheckM
[2024-01-24 13:55:46,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014262665.1_ASM1426266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014262665.1_ASM1426266v1_genomic.fna/checkm_input GCF_014262665.1_ASM1426266v1_genomic.fna/checkm_result
[2024-01-24 13:56:13,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:13,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:13,383] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:13,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:13,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014262665.1_ASM1426266v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:13,384] [INFO] Task started: Blastn
[2024-01-24 13:56:13,385] [INFO] Running command: blastn -query GCF_014262665.1_ASM1426266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66bdd6fd-9862-40d9-859c-a0992dd9ac20/dqc_reference/reference_markers_gtdb.fasta -out GCF_014262665.1_ASM1426266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:14,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:14,412] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:14,412] [INFO] Target genome list was writen to GCF_014262665.1_ASM1426266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:14,436] [INFO] Task started: fastANI
[2024-01-24 13:56:14,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc60f1b-37af-4b86-8767-e364246a0af6/GCF_014262665.1_ASM1426266v1_genomic.fna.gz --refList GCF_014262665.1_ASM1426266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014262665.1_ASM1426266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:25,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:25,039] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:25,039] [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_014262665.1	s__Corynebacterium anserum	100.0	735	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.46	99.46	0.99	0.99	2	conclusive
GCF_009026825.1	s__Corynebacterium sp009026825	79.1618	225	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177535.2	s__Corynebacterium resistens	78.8325	108	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	78.5993	107	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000767255.1	s__Corynebacterium auriscanis	78.5315	91	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.87	97.87	0.94	0.94	2	-
GCF_900232865.1	s__Corynebacterium dentalis	78.213	145	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_001941445.1	s__Corynebacterium aquilae	78.1646	53	736	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	78.0941	139	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	78.0539	53	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_001807485.1	s__Corynebacterium sp001807485	77.7752	107	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCA_019114175.1	s__Corynebacterium gallistercoris	77.5664	106	736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209905.1	s__Corynebacterium sp019209905	76.9616	50	736	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 13:56:25,041] [INFO] GTDB search result was written to GCF_014262665.1_ASM1426266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:25,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:25,045] [INFO] DFAST_QC result json was written to GCF_014262665.1_ASM1426266v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:25,046] [INFO] DFAST_QC completed!
[2024-01-24 13:56:25,046] [INFO] Total running time: 0h0m60s