[2024-01-24 13:27:46,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference
[2024-01-24 13:27:47,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,533] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d74e054-3cdc-47bf-906f-1565098db0b8/GCF_000236705.1_ASM23670v1_genomic.fna.gz | prodigal -d GCF_000236705.1_ASM23670v1_genomic.fna/cds.fna -a GCF_000236705.1_ASM23670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:05,603] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:05,603] [INFO] Task started: HMMsearch
[2024-01-24 13:28:05,603] [INFO] Running command: hmmsearch --tblout GCF_000236705.1_ASM23670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/reference_markers.hmm GCF_000236705.1_ASM23670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:05,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:05,920] [INFO] Found 6/6 markers.
[2024-01-24 13:28:05,966] [INFO] Query marker FASTA was written to GCF_000236705.1_ASM23670v1_genomic.fna/markers.fasta
[2024-01-24 13:28:05,967] [INFO] Task started: Blastn
[2024-01-24 13:28:05,967] [INFO] Running command: blastn -query GCF_000236705.1_ASM23670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/reference_markers.fasta -out GCF_000236705.1_ASM23670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:06,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:06,626] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:06,626] [INFO] Target genome list was writen to GCF_000236705.1_ASM23670v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:06,635] [INFO] Task started: fastANI
[2024-01-24 13:28:06,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d74e054-3cdc-47bf-906f-1565098db0b8/GCF_000236705.1_ASM23670v1_genomic.fna.gz --refList GCF_000236705.1_ASM23670v1_genomic.fna/target_genomes.txt --output GCF_000236705.1_ASM23670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:19,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:19,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:19,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:19,156] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:19,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:19,156] [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
Owenweeksia hongkongensis	strain=DSM 17368	GCA_000236705.1	253245	253245	type	True	100.0	1333	1333	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:28:19,158] [INFO] DFAST Taxonomy check result was written to GCF_000236705.1_ASM23670v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:19,158] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:19,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:19,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/checkm_data
[2024-01-24 13:28:19,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:19,207] [INFO] Task started: CheckM
[2024-01-24 13:28:19,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000236705.1_ASM23670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000236705.1_ASM23670v1_genomic.fna/checkm_input GCF_000236705.1_ASM23670v1_genomic.fna/checkm_result
[2024-01-24 13:29:13,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:13,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:13,577] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:13,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:13,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000236705.1_ASM23670v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:13,579] [INFO] Task started: Blastn
[2024-01-24 13:29:13,579] [INFO] Running command: blastn -query GCF_000236705.1_ASM23670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb601301-03ea-471f-bb5d-6804faafc040/dqc_reference/reference_markers_gtdb.fasta -out GCF_000236705.1_ASM23670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:14,322] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:14,327] [INFO] Selected 28 target genomes.
[2024-01-24 13:29:14,328] [INFO] Target genome list was writen to GCF_000236705.1_ASM23670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:14,372] [INFO] Task started: fastANI
[2024-01-24 13:29:14,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d74e054-3cdc-47bf-906f-1565098db0b8/GCF_000236705.1_ASM23670v1_genomic.fna.gz --refList GCF_000236705.1_ASM23670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000236705.1_ASM23670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:28,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:28,814] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:28,814] [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_000236705.1	s__Owenweeksia hongkongensis	100.0	1332	1333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Owenweeksia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002501205.1	s__Croceimicrobium sp002501205	76.0885	55	1333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Croceimicrobium	95.0	99.91	99.91	0.95	0.95	2	-
GCA_002695025.1	s__Owenweeksia sp002695025	76.0869	68	1333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Owenweeksia	95.0	99.94	99.87	0.98	0.96	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:28,816] [INFO] GTDB search result was written to GCF_000236705.1_ASM23670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:28,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:28,819] [INFO] DFAST_QC result json was written to GCF_000236705.1_ASM23670v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:28,819] [INFO] DFAST_QC completed!
[2024-01-24 13:29:28,819] [INFO] Total running time: 0h1m43s