[2024-01-24 11:51:06,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,949] [INFO] DQC Reference Directory: /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference
[2024-01-24 11:51:08,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,215] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,216] [INFO] Running command: gunzip -c /var/lib/cwl/stgde290145-6e3c-4c50-9eed-702a26344407/GCF_024453835.1_ASM2445383v1_genomic.fna.gz | prodigal -d GCF_024453835.1_ASM2445383v1_genomic.fna/cds.fna -a GCF_024453835.1_ASM2445383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:15,718] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:15,719] [INFO] Task started: HMMsearch
[2024-01-24 11:51:15,719] [INFO] Running command: hmmsearch --tblout GCF_024453835.1_ASM2445383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/reference_markers.hmm GCF_024453835.1_ASM2445383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:15,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:15,988] [INFO] Found 6/6 markers.
[2024-01-24 11:51:16,022] [INFO] Query marker FASTA was written to GCF_024453835.1_ASM2445383v1_genomic.fna/markers.fasta
[2024-01-24 11:51:16,022] [INFO] Task started: Blastn
[2024-01-24 11:51:16,022] [INFO] Running command: blastn -query GCF_024453835.1_ASM2445383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/reference_markers.fasta -out GCF_024453835.1_ASM2445383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:17,033] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:17,037] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:17,038] [INFO] Target genome list was writen to GCF_024453835.1_ASM2445383v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:17,077] [INFO] Task started: fastANI
[2024-01-24 11:51:17,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgde290145-6e3c-4c50-9eed-702a26344407/GCF_024453835.1_ASM2445383v1_genomic.fna.gz --refList GCF_024453835.1_ASM2445383v1_genomic.fna/target_genomes.txt --output GCF_024453835.1_ASM2445383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:22,955] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:22,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:22,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:22,979] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:22,980] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:22,980] [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 appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	81.4009	471	779	95	below_threshold
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	81.2282	460	779	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	80.0598	357	779	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.9995	368	779	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	79.8897	320	779	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	79.8846	339	779	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.8297	305	779	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	79.8006	324	779	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	79.7929	316	779	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	79.7028	322	779	95	below_threshold
Corynebacterium tuscaniense	strain=CCUG 51321T	GCA_008693065.1	302449	302449	type	True	79.6198	310	779	95	below_threshold
Corynebacterium coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	79.0845	282	779	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.6921	179	779	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	78.6904	177	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:22,982] [INFO] DFAST Taxonomy check result was written to GCF_024453835.1_ASM2445383v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:22,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:22,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:22,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/checkm_data
[2024-01-24 11:51:22,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:23,008] [INFO] Task started: CheckM
[2024-01-24 11:51:23,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024453835.1_ASM2445383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024453835.1_ASM2445383v1_genomic.fna/checkm_input GCF_024453835.1_ASM2445383v1_genomic.fna/checkm_result
[2024-01-24 11:51:50,382] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:50,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:50,407] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:50,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:50,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024453835.1_ASM2445383v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:50,408] [INFO] Task started: Blastn
[2024-01-24 11:51:50,408] [INFO] Running command: blastn -query GCF_024453835.1_ASM2445383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga52339f7-c62c-4791-b6da-254a94cfd199/dqc_reference/reference_markers_gtdb.fasta -out GCF_024453835.1_ASM2445383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:51,833] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:51,837] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:51,837] [INFO] Target genome list was writen to GCF_024453835.1_ASM2445383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:51,850] [INFO] Task started: fastANI
[2024-01-24 11:51:51,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgde290145-6e3c-4c50-9eed-702a26344407/GCF_024453835.1_ASM2445383v1_genomic.fna.gz --refList GCF_024453835.1_ASM2445383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024453835.1_ASM2445383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:56,755] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:56,766] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:56,766] [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_000143825.1	s__Corynebacterium genitalium_A	99.9952	773	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900618065.1	s__Corynebacterium sp900618065	90.2479	688	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156665.1	s__Corynebacterium appendicis	81.4154	470	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017942225.1	s__Corynebacterium sp017942225	81.2465	467	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155535.1	s__Corynebacterium urinipleomorphum	81.2101	462	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411315.1	s__Corynebacterium senegalense	79.9701	368	779	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	79.944	321	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	79.663	320	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900105505.1	s__Corynebacterium coyleae	79.0846	283	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.6052	178	779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:56,769] [INFO] GTDB search result was written to GCF_024453835.1_ASM2445383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:56,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:56,773] [INFO] DFAST_QC result json was written to GCF_024453835.1_ASM2445383v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:56,773] [INFO] DFAST_QC completed!
[2024-01-24 11:51:56,773] [INFO] Total running time: 0h0m50s