[2024-01-24 12:13:25,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:25,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:25,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference
[2024-01-24 12:13:26,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,801] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,802] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd7085f8-ea6e-4f76-90c3-ea8bad43f0de/GCF_000372085.1_ASM37208v1_genomic.fna.gz | prodigal -d GCF_000372085.1_ASM37208v1_genomic.fna/cds.fna -a GCF_000372085.1_ASM37208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:32,885] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:32,886] [INFO] Task started: HMMsearch
[2024-01-24 12:13:32,886] [INFO] Running command: hmmsearch --tblout GCF_000372085.1_ASM37208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/reference_markers.hmm GCF_000372085.1_ASM37208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:33,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:33,109] [INFO] Found 6/6 markers.
[2024-01-24 12:13:33,140] [INFO] Query marker FASTA was written to GCF_000372085.1_ASM37208v1_genomic.fna/markers.fasta
[2024-01-24 12:13:33,141] [INFO] Task started: Blastn
[2024-01-24 12:13:33,141] [INFO] Running command: blastn -query GCF_000372085.1_ASM37208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/reference_markers.fasta -out GCF_000372085.1_ASM37208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:33,971] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:33,974] [INFO] Selected 17 target genomes.
[2024-01-24 12:13:33,974] [INFO] Target genome list was writen to GCF_000372085.1_ASM37208v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:34,006] [INFO] Task started: fastANI
[2024-01-24 12:13:34,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7085f8-ea6e-4f76-90c3-ea8bad43f0de/GCF_000372085.1_ASM37208v1_genomic.fna.gz --refList GCF_000372085.1_ASM37208v1_genomic.fna/target_genomes.txt --output GCF_000372085.1_ASM37208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:43,537] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:43,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:43,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:43,551] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:43,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:43,552] [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	100.0	651	651	95	conclusive
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	80.2241	408	651	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	79.8061	338	651	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	79.7977	340	651	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	79.3951	318	651	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	79.037	274	651	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	78.8709	244	651	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	78.719	260	651	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	78.6944	239	651	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	78.6706	255	651	95	below_threshold
Corynebacterium imitans	strain=NCTC13015	GCA_900187215.1	156978	156978	type	True	78.6421	255	651	95	below_threshold
Corynebacterium imitans	strain=DSM 44264	GCA_000739455.1	156978	156978	type	True	78.6103	247	651	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	78.4496	267	651	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	78.1844	234	651	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	75.6248	65	651	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	75.4151	56	651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:43,555] [INFO] DFAST Taxonomy check result was written to GCF_000372085.1_ASM37208v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:43,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:43,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:43,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/checkm_data
[2024-01-24 12:13:43,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:43,593] [INFO] Task started: CheckM
[2024-01-24 12:13:43,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372085.1_ASM37208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372085.1_ASM37208v1_genomic.fna/checkm_input GCF_000372085.1_ASM37208v1_genomic.fna/checkm_result
[2024-01-24 12:14:07,766] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:07,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:07,787] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:07,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:07,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372085.1_ASM37208v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:07,788] [INFO] Task started: Blastn
[2024-01-24 12:14:07,788] [INFO] Running command: blastn -query GCF_000372085.1_ASM37208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e3933e-5c2d-4c3e-8cfe-153f0ece05fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372085.1_ASM37208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:08,970] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:08,973] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:08,973] [INFO] Target genome list was writen to GCF_000372085.1_ASM37208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:08,987] [INFO] Task started: fastANI
[2024-01-24 12:14:08,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd7085f8-ea6e-4f76-90c3-ea8bad43f0de/GCF_000372085.1_ASM37208v1_genomic.fna.gz --refList GCF_000372085.1_ASM37208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372085.1_ASM37208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:18,778] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:18,795] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:18,795] [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	100.0	651	651	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	80.2098	409	651	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	79.8061	338	651	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	79.6606	347	651	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	79.3951	318	651	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	79.0605	272	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	78.8706	245	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	78.7958	279	651	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	78.7168	260	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCF_900176865.1	s__Corynebacterium fournieri	78.6784	240	651	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	78.6115	247	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014490595.1	s__Corynebacterium sp014490595	78.5923	207	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCA_900156035.1	s__Corynebacterium afermentans	78.4991	272	651	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	78.1844	234	651	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	77.465	159	651	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	75.6248	65	651	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	75.5265	76	651	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 12:14:18,797] [INFO] GTDB search result was written to GCF_000372085.1_ASM37208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:18,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:18,801] [INFO] DFAST_QC result json was written to GCF_000372085.1_ASM37208v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:18,802] [INFO] DFAST_QC completed!
[2024-01-24 12:14:18,802] [INFO] Total running time: 0h0m53s