[2024-01-24 11:05:22,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:22,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:22,559] [INFO] DQC Reference Directory: /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference
[2024-01-24 11:05:25,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,539] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,540] [INFO] Running command: gunzip -c /var/lib/cwl/stgc52f7c31-f8bb-4a8f-8192-49201e46c9df/GCF_015351405.1_ASM1535140v1_genomic.fna.gz | prodigal -d GCF_015351405.1_ASM1535140v1_genomic.fna/cds.fna -a GCF_015351405.1_ASM1535140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:33,097] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:33,098] [INFO] Task started: HMMsearch
[2024-01-24 11:05:33,098] [INFO] Running command: hmmsearch --tblout GCF_015351405.1_ASM1535140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/reference_markers.hmm GCF_015351405.1_ASM1535140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:33,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:33,313] [INFO] Found 6/6 markers.
[2024-01-24 11:05:33,336] [INFO] Query marker FASTA was written to GCF_015351405.1_ASM1535140v1_genomic.fna/markers.fasta
[2024-01-24 11:05:33,336] [INFO] Task started: Blastn
[2024-01-24 11:05:33,336] [INFO] Running command: blastn -query GCF_015351405.1_ASM1535140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/reference_markers.fasta -out GCF_015351405.1_ASM1535140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:34,189] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:34,193] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:34,194] [INFO] Target genome list was writen to GCF_015351405.1_ASM1535140v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:34,202] [INFO] Task started: fastANI
[2024-01-24 11:05:34,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52f7c31-f8bb-4a8f-8192-49201e46c9df/GCF_015351405.1_ASM1535140v1_genomic.fna.gz --refList GCF_015351405.1_ASM1535140v1_genomic.fna/target_genomes.txt --output GCF_015351405.1_ASM1535140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:41,902] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:41,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:41,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:41,921] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:41,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:41,921] [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 suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	100.0	739	739	95	conclusive
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	80.7212	482	739	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.0271	247	739	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	78.8148	258	739	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.4272	210	739	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	78.4251	235	739	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.4185	228	739	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.2382	196	739	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	78.2141	196	739	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	78.1783	147	739	95	below_threshold
Corynebacterium heidelbergense	strain=DSM 104638	GCA_003285565.1	2055947	2055947	type	True	78.0963	154	739	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	77.9112	99	739	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	77.5277	106	739	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.3372	140	739	95	below_threshold
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	77.3129	89	739	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.2631	124	739	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	76.4433	70	739	95	below_threshold
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	76.0922	76	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:41,926] [INFO] DFAST Taxonomy check result was written to GCF_015351405.1_ASM1535140v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:41,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:41,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:41,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/checkm_data
[2024-01-24 11:05:41,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:41,961] [INFO] Task started: CheckM
[2024-01-24 11:05:41,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015351405.1_ASM1535140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015351405.1_ASM1535140v1_genomic.fna/checkm_input GCF_015351405.1_ASM1535140v1_genomic.fna/checkm_result
[2024-01-24 11:06:09,180] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:09,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,201] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:09,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:09,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015351405.1_ASM1535140v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:09,203] [INFO] Task started: Blastn
[2024-01-24 11:06:09,203] [INFO] Running command: blastn -query GCF_015351405.1_ASM1535140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga538768d-bbcc-4c4e-85ed-d6fb307bc5fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_015351405.1_ASM1535140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:10,444] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:10,449] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:10,449] [INFO] Target genome list was writen to GCF_015351405.1_ASM1535140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:10,463] [INFO] Task started: fastANI
[2024-01-24 11:06:10,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52f7c31-f8bb-4a8f-8192-49201e46c9df/GCF_015351405.1_ASM1535140v1_genomic.fna.gz --refList GCF_015351405.1_ASM1535140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015351405.1_ASM1535140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:19,577] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,594] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:19,595] [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_015351405.1	s__Corynebacterium sp015351405	100.0	739	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900232865.1	s__Corynebacterium dentalis	80.7111	484	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_009026825.1	s__Corynebacterium sp009026825	79.0085	248	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000525655.1	s__Corynebacterium falsenii	78.743	264	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_014490575.1	s__Corynebacterium sp014490575	78.4272	210	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.4084	251	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807485.1	s__Corynebacterium sp001807485	78.4072	249	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000163435.1	s__Corynebacterium jeikeium	78.401	229	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	78.3094	245	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.1423	199	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_000177535.2	s__Corynebacterium resistens	78.1079	145	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285565.1	s__Corynebacterium heidelbergense	78.0963	154	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	-
GCF_001941445.1	s__Corynebacterium aquilae	77.9112	99	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815985.1	s__Corynebacterium sp001815985	77.6724	225	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_900103625.1	s__Corynebacterium mycetoides	77.4985	107	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120175.1	s__Corynebacterium faecigallinarum	77.413	160	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.3164	141	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375365.1	s__Corynebacterium mastitidis	77.2631	124	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCA_003600225.1	s__QZFT01 sp003600225	75.9842	65	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__QZFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119875.1	s__Dietzia intestinigallinarum	75.7839	61	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,596] [INFO] GTDB search result was written to GCF_015351405.1_ASM1535140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:19,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:19,601] [INFO] DFAST_QC result json was written to GCF_015351405.1_ASM1535140v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:19,602] [INFO] DFAST_QC completed!
[2024-01-24 11:06:19,602] [INFO] Total running time: 0h0m57s