[2024-01-25 19:30:21,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:30:21,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:30:21,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference
[2024-01-25 19:30:22,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:30:22,646] [INFO] Task started: Prodigal
[2024-01-25 19:30:22,646] [INFO] Running command: gunzip -c /var/lib/cwl/stge18a433f-ca65-4e19-a384-b2f828b07554/GCF_000379705.1_ASM37970v1_genomic.fna.gz | prodigal -d GCF_000379705.1_ASM37970v1_genomic.fna/cds.fna -a GCF_000379705.1_ASM37970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:30:26,574] [INFO] Task succeeded: Prodigal
[2024-01-25 19:30:26,575] [INFO] Task started: HMMsearch
[2024-01-25 19:30:26,575] [INFO] Running command: hmmsearch --tblout GCF_000379705.1_ASM37970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/reference_markers.hmm GCF_000379705.1_ASM37970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:30:26,736] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:30:26,737] [INFO] Found 6/6 markers.
[2024-01-25 19:30:26,756] [INFO] Query marker FASTA was written to GCF_000379705.1_ASM37970v1_genomic.fna/markers.fasta
[2024-01-25 19:30:26,756] [INFO] Task started: Blastn
[2024-01-25 19:30:26,756] [INFO] Running command: blastn -query GCF_000379705.1_ASM37970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/reference_markers.fasta -out GCF_000379705.1_ASM37970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:27,445] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:27,448] [INFO] Selected 22 target genomes.
[2024-01-25 19:30:27,449] [INFO] Target genome list was writen to GCF_000379705.1_ASM37970v1_genomic.fna/target_genomes.txt
[2024-01-25 19:30:27,484] [INFO] Task started: fastANI
[2024-01-25 19:30:27,484] [INFO] Running command: fastANI --query /var/lib/cwl/stge18a433f-ca65-4e19-a384-b2f828b07554/GCF_000379705.1_ASM37970v1_genomic.fna.gz --refList GCF_000379705.1_ASM37970v1_genomic.fna/target_genomes.txt --output GCF_000379705.1_ASM37970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:30:35,005] [INFO] Task succeeded: fastANI
[2024-01-25 19:30:35,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:30:35,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:30:35,011] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:30:35,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:30:35,011] [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 caspium	strain=DSM 44850	GCA_000379705.1	234828	234828	type	True	100.0	609	610	95	conclusive
Corynebacterium callunae	strain=DSM 20147	GCA_000420585.1	1721	1721	type	True	77.118	51	610	95	below_threshold
Corynebacterium callunae	strain=DSM 20147	GCA_000344785.1	1721	1721	type	True	77.0597	50	610	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	76.8996	57	610	95	below_threshold
Corynebacterium renale	strain=DSM 20688	GCA_002563965.1	1724	1724	type	True	76.8996	57	610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:30:35,014] [INFO] DFAST Taxonomy check result was written to GCF_000379705.1_ASM37970v1_genomic.fna/tc_result.tsv
[2024-01-25 19:30:35,014] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:30:35,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:30:35,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/checkm_data
[2024-01-25 19:30:35,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:30:35,036] [INFO] Task started: CheckM
[2024-01-25 19:30:35,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000379705.1_ASM37970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000379705.1_ASM37970v1_genomic.fna/checkm_input GCF_000379705.1_ASM37970v1_genomic.fna/checkm_result
[2024-01-25 19:30:51,917] [INFO] Task succeeded: CheckM
[2024-01-25 19:30:51,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:30:51,934] [INFO] ===== Completeness check finished =====
[2024-01-25 19:30:51,934] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:30:51,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000379705.1_ASM37970v1_genomic.fna/markers.fasta)
[2024-01-25 19:30:51,935] [INFO] Task started: Blastn
[2024-01-25 19:30:51,935] [INFO] Running command: blastn -query GCF_000379705.1_ASM37970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b077fbd-40fd-4b57-b93b-d4bf84ed660e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000379705.1_ASM37970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:52,909] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:52,915] [INFO] Selected 22 target genomes.
[2024-01-25 19:30:52,915] [INFO] Target genome list was writen to GCF_000379705.1_ASM37970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:30:52,950] [INFO] Task started: fastANI
[2024-01-25 19:30:52,951] [INFO] Running command: fastANI --query /var/lib/cwl/stge18a433f-ca65-4e19-a384-b2f828b07554/GCF_000379705.1_ASM37970v1_genomic.fna.gz --refList GCF_000379705.1_ASM37970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000379705.1_ASM37970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:31:01,384] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:01,388] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:31:01,388] [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_000379705.1	s__Corynebacterium caspium	100.0	609	610	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_000344785.1	s__Corynebacterium callunae	77.0597	50	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563965.1	s__Corynebacterium renale	76.8996	57	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:31:01,390] [INFO] GTDB search result was written to GCF_000379705.1_ASM37970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:31:01,390] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:31:01,392] [INFO] DFAST_QC result json was written to GCF_000379705.1_ASM37970v1_genomic.fna/dqc_result.json
[2024-01-25 19:31:01,392] [INFO] DFAST_QC completed!
[2024-01-25 19:31:01,392] [INFO] Total running time: 0h0m40s