[2024-01-24 12:23:03,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference
[2024-01-24 12:23:05,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,282] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,282] [INFO] Running command: gunzip -c /var/lib/cwl/stgda7f97dc-01b4-427f-98ce-ddb7a181555f/GCF_030408775.1_ASM3040877v1_genomic.fna.gz | prodigal -d GCF_030408775.1_ASM3040877v1_genomic.fna/cds.fna -a GCF_030408775.1_ASM3040877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,530] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,531] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,531] [INFO] Running command: hmmsearch --tblout GCF_030408775.1_ASM3040877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/reference_markers.hmm GCF_030408775.1_ASM3040877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:13,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:13,718] [INFO] Found 6/6 markers.
[2024-01-24 12:23:13,743] [INFO] Query marker FASTA was written to GCF_030408775.1_ASM3040877v1_genomic.fna/markers.fasta
[2024-01-24 12:23:13,743] [INFO] Task started: Blastn
[2024-01-24 12:23:13,743] [INFO] Running command: blastn -query GCF_030408775.1_ASM3040877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/reference_markers.fasta -out GCF_030408775.1_ASM3040877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,783] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,786] [INFO] Selected 7 target genomes.
[2024-01-24 12:23:14,787] [INFO] Target genome list was writen to GCF_030408775.1_ASM3040877v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,797] [INFO] Task started: fastANI
[2024-01-24 12:23:14,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7f97dc-01b4-427f-98ce-ddb7a181555f/GCF_030408775.1_ASM3040877v1_genomic.fna.gz --refList GCF_030408775.1_ASM3040877v1_genomic.fna/target_genomes.txt --output GCF_030408775.1_ASM3040877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:18,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:18,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:18,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:18,890] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:18,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:18,891] [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 fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	99.7299	755	796	95	conclusive
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	87.9042	704	796	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	87.895	683	796	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	87.3849	646	796	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	86.0873	640	796	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	84.2826	528	796	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	83.8864	588	796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:18,892] [INFO] DFAST Taxonomy check result was written to GCF_030408775.1_ASM3040877v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:18,893] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:18,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:18,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/checkm_data
[2024-01-24 12:23:18,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:18,920] [INFO] Task started: CheckM
[2024-01-24 12:23:18,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408775.1_ASM3040877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408775.1_ASM3040877v1_genomic.fna/checkm_input GCF_030408775.1_ASM3040877v1_genomic.fna/checkm_result
[2024-01-24 12:23:45,914] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:45,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,932] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:45,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:45,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408775.1_ASM3040877v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:45,933] [INFO] Task started: Blastn
[2024-01-24 12:23:45,933] [INFO] Running command: blastn -query GCF_030408775.1_ASM3040877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625499a3-fda0-4e55-b852-0b107fcb3c70/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408775.1_ASM3040877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:47,510] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:47,513] [INFO] Selected 6 target genomes.
[2024-01-24 12:23:47,513] [INFO] Target genome list was writen to GCF_030408775.1_ASM3040877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:47,517] [INFO] Task started: fastANI
[2024-01-24 12:23:47,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7f97dc-01b4-427f-98ce-ddb7a181555f/GCF_030408775.1_ASM3040877v1_genomic.fna.gz --refList GCF_030408775.1_ASM3040877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408775.1_ASM3040877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:50,978] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:50,985] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:50,985] [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_900176865.1	s__Corynebacterium fournieri	99.7299	755	796	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_013978595.1	s__Corynebacterium haemomassiliense	87.8975	703	796	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	87.895	683	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	87.6375	655	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	87.5019	654	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCA_014490595.1	s__Corynebacterium sp014490595	86.0021	535	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,986] [INFO] GTDB search result was written to GCF_030408775.1_ASM3040877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:50,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:50,989] [INFO] DFAST_QC result json was written to GCF_030408775.1_ASM3040877v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:50,990] [INFO] DFAST_QC completed!
[2024-01-24 12:23:50,990] [INFO] Total running time: 0h0m47s