[2024-01-24 11:09:50,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference
[2024-01-24 11:09:53,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,311] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,312] [INFO] Running command: gunzip -c /var/lib/cwl/stge1c7a32e-905e-4124-af8e-aa718b96906d/GCF_002847405.1_ASM284740v1_genomic.fna.gz | prodigal -d GCF_002847405.1_ASM284740v1_genomic.fna/cds.fna -a GCF_002847405.1_ASM284740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:04,007] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:04,008] [INFO] Task started: HMMsearch
[2024-01-24 11:10:04,008] [INFO] Running command: hmmsearch --tblout GCF_002847405.1_ASM284740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/reference_markers.hmm GCF_002847405.1_ASM284740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:04,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:04,236] [INFO] Found 6/6 markers.
[2024-01-24 11:10:04,267] [INFO] Query marker FASTA was written to GCF_002847405.1_ASM284740v1_genomic.fna/markers.fasta
[2024-01-24 11:10:04,268] [INFO] Task started: Blastn
[2024-01-24 11:10:04,268] [INFO] Running command: blastn -query GCF_002847405.1_ASM284740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/reference_markers.fasta -out GCF_002847405.1_ASM284740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:05,065] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:05,068] [INFO] Selected 6 target genomes.
[2024-01-24 11:10:05,069] [INFO] Target genome list was writen to GCF_002847405.1_ASM284740v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:05,074] [INFO] Task started: fastANI
[2024-01-24 11:10:05,074] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c7a32e-905e-4124-af8e-aa718b96906d/GCF_002847405.1_ASM284740v1_genomic.fna.gz --refList GCF_002847405.1_ASM284740v1_genomic.fna/target_genomes.txt --output GCF_002847405.1_ASM284740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:10,112] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:10,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:10,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:10,126] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:10:10,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:10,127] [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 glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	100.0	1104	1105	95	conclusive
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	99.9914	1101	1105	95	conclusive
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	99.9816	1101	1105	95	conclusive
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	97.6196	956	1105	95	conclusive
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	85.9266	896	1105	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	83.9452	768	1105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:10,128] [INFO] DFAST Taxonomy check result was written to GCF_002847405.1_ASM284740v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:10,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:10,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:10,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/checkm_data
[2024-01-24 11:10:10,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:10,168] [INFO] Task started: CheckM
[2024-01-24 11:10:10,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002847405.1_ASM284740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002847405.1_ASM284740v1_genomic.fna/checkm_input GCF_002847405.1_ASM284740v1_genomic.fna/checkm_result
[2024-01-24 11:10:45,965] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:45,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:45,982] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:45,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:45,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002847405.1_ASM284740v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:45,982] [INFO] Task started: Blastn
[2024-01-24 11:10:45,982] [INFO] Running command: blastn -query GCF_002847405.1_ASM284740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg748586e2-2291-43fa-b9f1-ef2ff46f22ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_002847405.1_ASM284740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:47,168] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:47,172] [INFO] Selected 7 target genomes.
[2024-01-24 11:10:47,172] [INFO] Target genome list was writen to GCF_002847405.1_ASM284740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:47,217] [INFO] Task started: fastANI
[2024-01-24 11:10:47,218] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c7a32e-905e-4124-af8e-aa718b96906d/GCF_002847405.1_ASM284740v1_genomic.fna.gz --refList GCF_002847405.1_ASM284740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002847405.1_ASM284740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:10:52,616] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:52,625] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:10:52,625] [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_000011325.1	s__Corynebacterium glutamicum	99.9914	1101	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	conclusive
GCF_002355155.1	s__Corynebacterium suranareeae	85.936	897	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643015.1	s__Corynebacterium crudilactis	83.9651	767	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277995.1	s__Corynebacterium deserti	83.4408	659	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344785.1	s__Corynebacterium callunae	81.0729	465	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000011305.1	s__Corynebacterium efficiens	79.2463	354	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	78.8447	181	1105	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 11:10:52,627] [INFO] GTDB search result was written to GCF_002847405.1_ASM284740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:10:52,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:10:52,630] [INFO] DFAST_QC result json was written to GCF_002847405.1_ASM284740v1_genomic.fna/dqc_result.json
[2024-01-24 11:10:52,630] [INFO] DFAST_QC completed!
[2024-01-24 11:10:52,630] [INFO] Total running time: 0h1m2s