[2024-01-24 13:32:42,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference
[2024-01-24 13:32:43,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,735] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,735] [INFO] Running command: gunzip -c /var/lib/cwl/stgecbf4aa2-87ec-4318-85ca-c4712b0ed1d3/GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/cds.fna -a GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:52,831] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:52,831] [INFO] Task started: HMMsearch
[2024-01-24 13:32:52,831] [INFO] Running command: hmmsearch --tblout GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/reference_markers.hmm GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:53,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:53,073] [INFO] Found 6/6 markers.
[2024-01-24 13:32:53,110] [INFO] Query marker FASTA was written to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:53,110] [INFO] Task started: Blastn
[2024-01-24 13:32:53,110] [INFO] Running command: blastn -query GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/reference_markers.fasta -out GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,910] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,913] [INFO] Selected 6 target genomes.
[2024-01-24 13:32:53,913] [INFO] Target genome list was writen to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:53,918] [INFO] Task started: fastANI
[2024-01-24 13:32:53,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbf4aa2-87ec-4318-85ca-c4712b0ed1d3/GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna.gz --refList GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:57,555] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:57,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:57,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:57,562] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:57,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:57,563] [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 cystitidis	strain=DSM 20524	GCA_900111265.1	35757	35757	type	True	100.0	956	959	95	conclusive
Corynebacterium cystitidis	strain=NCTC11863	GCA_900187295.1	35757	35757	type	True	99.9875	958	959	95	conclusive
Corynebacterium pilosum	strain=CIP103422	GCA_001044155.1	35756	35756	type	True	80.5305	505	959	95	below_threshold
Corynebacterium pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	80.5283	509	959	95	below_threshold
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	80.4384	504	959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,564] [INFO] DFAST Taxonomy check result was written to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:57,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:57,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:57,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/checkm_data
[2024-01-24 13:32:57,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:57,600] [INFO] Task started: CheckM
[2024-01-24 13:32:57,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/checkm_input GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:33:29,056] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:29,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:29,073] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:29,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:29,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:33:29,074] [INFO] Task started: Blastn
[2024-01-24 13:33:29,074] [INFO] Running command: blastn -query GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ac18b4-4958-4989-9cca-0e4f3d7fc7e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:30,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:30,173] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:30,173] [INFO] Target genome list was writen to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:30,204] [INFO] Task started: fastANI
[2024-01-24 13:33:30,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgecbf4aa2-87ec-4318-85ca-c4712b0ed1d3/GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna.gz --refList GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:37,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:37,091] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:37,091] [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_900187295.1	s__Corynebacterium cystitidis	99.9875	958	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000373805.1	s__Corynebacterium pilosum	80.4499	503	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	-
GCF_000379425.1	s__Corynebacterium lubricantis	78.2592	215	959	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	77.655	131	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900105505.1	s__Corynebacterium coyleae	77.6537	139	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_015351335.1	s__Corynebacterium lipophilum	77.6248	144	959	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	77.5855	160	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980815.1	s__Corynebacterium camporealensis	77.5792	106	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_003693265.1	s__Corynebacterium gottingense	77.4928	138	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.4445	131	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	77.3456	140	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	77.3061	150	959	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006334925.1	s__Corynebacterium tapiri	77.1861	122	959	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	77.1631	152	959	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 13:33:37,093] [INFO] GTDB search result was written to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:37,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:37,097] [INFO] DFAST_QC result json was written to GCF_900111265.1_IMG-taxon_2599185266_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:33:37,097] [INFO] DFAST_QC completed!
[2024-01-24 13:33:37,097] [INFO] Total running time: 0h0m55s