[2024-01-24 12:06:13,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,864] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference
[2024-01-24 12:06:15,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,224] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d0ec97-05ba-4aba-b25c-033e9dc1e215/GCF_001856685.1_ASM185668v1_genomic.fna.gz | prodigal -d GCF_001856685.1_ASM185668v1_genomic.fna/cds.fna -a GCF_001856685.1_ASM185668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:21,502] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:21,502] [INFO] Task started: HMMsearch
[2024-01-24 12:06:21,503] [INFO] Running command: hmmsearch --tblout GCF_001856685.1_ASM185668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/reference_markers.hmm GCF_001856685.1_ASM185668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:21,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:21,805] [INFO] Found 6/6 markers.
[2024-01-24 12:06:21,829] [INFO] Query marker FASTA was written to GCF_001856685.1_ASM185668v1_genomic.fna/markers.fasta
[2024-01-24 12:06:21,829] [INFO] Task started: Blastn
[2024-01-24 12:06:21,830] [INFO] Running command: blastn -query GCF_001856685.1_ASM185668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/reference_markers.fasta -out GCF_001856685.1_ASM185668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:22,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:22,475] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:22,475] [INFO] Target genome list was writen to GCF_001856685.1_ASM185668v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:22,513] [INFO] Task started: fastANI
[2024-01-24 12:06:22,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d0ec97-05ba-4aba-b25c-033e9dc1e215/GCF_001856685.1_ASM185668v1_genomic.fna.gz --refList GCF_001856685.1_ASM185668v1_genomic.fna/target_genomes.txt --output GCF_001856685.1_ASM185668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:33,668] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:33,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:33,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:33,674] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:33,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:33,674] [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
Boudabousia tangfeifanii	strain=VUL4_3	GCA_001856685.1	1912795	1912795	type	True	100.0	735	735	95	conclusive
Boudabousia liubingyangii	strain=VUL4_1	GCA_001907245.1	1921764	1921764	type	True	81.3224	142	735	95	below_threshold
Boudabousia marimammalium	strain=DSM 15383	GCA_001936115.1	156892	156892	type	True	77.6406	77	735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:33,677] [INFO] DFAST Taxonomy check result was written to GCF_001856685.1_ASM185668v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:33,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:33,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:33,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/checkm_data
[2024-01-24 12:06:33,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:33,704] [INFO] Task started: CheckM
[2024-01-24 12:06:33,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001856685.1_ASM185668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001856685.1_ASM185668v1_genomic.fna/checkm_input GCF_001856685.1_ASM185668v1_genomic.fna/checkm_result
[2024-01-24 12:06:58,671] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:58,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:58,696] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:58,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:58,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001856685.1_ASM185668v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:58,698] [INFO] Task started: Blastn
[2024-01-24 12:06:58,698] [INFO] Running command: blastn -query GCF_001856685.1_ASM185668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34022e95-965e-4292-8e2b-d29d98bc3ecf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001856685.1_ASM185668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:59,586] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:59,589] [INFO] Selected 22 target genomes.
[2024-01-24 12:06:59,589] [INFO] Target genome list was writen to GCF_001856685.1_ASM185668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:59,635] [INFO] Task started: fastANI
[2024-01-24 12:06:59,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d0ec97-05ba-4aba-b25c-033e9dc1e215/GCF_001856685.1_ASM185668v1_genomic.fna.gz --refList GCF_001856685.1_ASM185668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001856685.1_ASM185668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:11,379] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:11,388] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:11,388] [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_001856685.1	s__Boudabousia tangfeifanii	100.0	735	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Boudabousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001907245.1	s__Boudabousia liubingyangii	81.3254	142	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Boudabousia	95.0	98.23	98.23	0.94	0.94	2	-
GCA_019218365.1	s__Boudabousia sp019218365	78.1597	64	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Boudabousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936115.1	s__Boudabousia marimammalium	77.6406	77	735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Boudabousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:11,391] [INFO] GTDB search result was written to GCF_001856685.1_ASM185668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:11,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:11,394] [INFO] DFAST_QC result json was written to GCF_001856685.1_ASM185668v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:11,394] [INFO] DFAST_QC completed!
[2024-01-24 12:07:11,394] [INFO] Total running time: 0h0m58s