[2024-01-24 13:21:59,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:59,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:59,815] [INFO] DQC Reference Directory: /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference
[2024-01-24 13:22:01,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:01,114] [INFO] Task started: Prodigal
[2024-01-24 13:22:01,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbda72d-0e8f-4653-becd-43320df504dc/GCF_030440535.1_ASM3044053v1_genomic.fna.gz | prodigal -d GCF_030440535.1_ASM3044053v1_genomic.fna/cds.fna -a GCF_030440535.1_ASM3044053v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:07,230] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:07,230] [INFO] Task started: HMMsearch
[2024-01-24 13:22:07,231] [INFO] Running command: hmmsearch --tblout GCF_030440535.1_ASM3044053v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/reference_markers.hmm GCF_030440535.1_ASM3044053v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:07,451] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:07,453] [INFO] Found 6/6 markers.
[2024-01-24 13:22:07,477] [INFO] Query marker FASTA was written to GCF_030440535.1_ASM3044053v1_genomic.fna/markers.fasta
[2024-01-24 13:22:07,478] [INFO] Task started: Blastn
[2024-01-24 13:22:07,478] [INFO] Running command: blastn -query GCF_030440535.1_ASM3044053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/reference_markers.fasta -out GCF_030440535.1_ASM3044053v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:08,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:08,322] [INFO] Selected 17 target genomes.
[2024-01-24 13:22:08,323] [INFO] Target genome list was writen to GCF_030440535.1_ASM3044053v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:08,360] [INFO] Task started: fastANI
[2024-01-24 13:22:08,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbda72d-0e8f-4653-becd-43320df504dc/GCF_030440535.1_ASM3044053v1_genomic.fna.gz --refList GCF_030440535.1_ASM3044053v1_genomic.fna/target_genomes.txt --output GCF_030440535.1_ASM3044053v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:18,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:18,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:18,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:18,072] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:18,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:18,073] [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 capitovis	strain=DSM 44611	GCA_000372085.1	131081	131081	type	True	99.9753	651	659	95	conclusive
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	80.6331	408	659	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	79.7986	353	659	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	79.683	342	659	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	79.566	328	659	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	79.0148	264	659	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	78.9929	267	659	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	78.9057	278	659	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	78.8963	248	659	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	78.7718	251	659	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	78.6151	258	659	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	78.6017	264	659	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	78.4027	267	659	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	78.1092	246	659	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	75.6774	60	659	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	75.6761	65	659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:18,074] [INFO] DFAST Taxonomy check result was written to GCF_030440535.1_ASM3044053v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:18,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:18,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:18,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/checkm_data
[2024-01-24 13:22:18,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:18,109] [INFO] Task started: CheckM
[2024-01-24 13:22:18,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030440535.1_ASM3044053v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030440535.1_ASM3044053v1_genomic.fna/checkm_input GCF_030440535.1_ASM3044053v1_genomic.fna/checkm_result
[2024-01-24 13:22:42,909] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:42,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:42,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:42,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:42,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030440535.1_ASM3044053v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:42,933] [INFO] Task started: Blastn
[2024-01-24 13:22:42,934] [INFO] Running command: blastn -query GCF_030440535.1_ASM3044053v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f7db44-8ecd-4572-8cc4-1d5de0123c83/dqc_reference/reference_markers_gtdb.fasta -out GCF_030440535.1_ASM3044053v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:44,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:44,188] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:44,189] [INFO] Target genome list was writen to GCF_030440535.1_ASM3044053v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:44,217] [INFO] Task started: fastANI
[2024-01-24 13:22:44,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbda72d-0e8f-4653-becd-43320df504dc/GCF_030440535.1_ASM3044053v1_genomic.fna.gz --refList GCF_030440535.1_ASM3044053v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030440535.1_ASM3044053v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:54,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:54,679] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:54,679] [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_000372085.1	s__Corynebacterium capitovis	99.9753	651	659	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_900411315.1	s__Corynebacterium senegalense	80.578	409	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105305.1	s__Corynebacterium timonense	79.8361	351	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCA_002339505.1	s__Corynebacterium sp002339505	79.7062	350	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	79.5445	328	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739455.1	s__Corynebacterium imitans	79.0247	264	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	78.9654	282	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	78.9221	277	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176865.1	s__Corynebacterium fournieri	78.8782	249	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014490595.1	s__Corynebacterium sp014490595	78.8049	218	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_015351335.1	s__Corynebacterium lipophilum	78.7542	250	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001831515.1	s__Corynebacterium sp001831515	78.7449	263	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCA_900156035.1	s__Corynebacterium afermentans	78.5884	268	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900156665.1	s__Corynebacterium appendicis	78.0893	248	659	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	77.5421	157	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_011045015.1	s__Streptomyces scabichelini	75.6761	65	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948485.1	s__Streptomyces sp017948485	75.5598	77	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:54,681] [INFO] GTDB search result was written to GCF_030440535.1_ASM3044053v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:54,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:54,686] [INFO] DFAST_QC result json was written to GCF_030440535.1_ASM3044053v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:54,686] [INFO] DFAST_QC completed!
[2024-01-24 13:22:54,686] [INFO] Total running time: 0h0m55s