[2024-01-25 18:59:50,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference
[2024-01-25 18:59:51,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,835] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,835] [INFO] Running command: gunzip -c /var/lib/cwl/stga643504a-db18-414c-bef6-a11f62af17fe/GCF_000178335.1_ASM17833v1_genomic.fna.gz | prodigal -d GCF_000178335.1_ASM17833v1_genomic.fna/cds.fna -a GCF_000178335.1_ASM17833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:54,837] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:54,838] [INFO] Task started: HMMsearch
[2024-01-25 18:59:54,838] [INFO] Running command: hmmsearch --tblout GCF_000178335.1_ASM17833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/reference_markers.hmm GCF_000178335.1_ASM17833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:55,011] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:55,012] [INFO] Found 6/6 markers.
[2024-01-25 18:59:55,025] [INFO] Query marker FASTA was written to GCF_000178335.1_ASM17833v1_genomic.fna/markers.fasta
[2024-01-25 18:59:55,026] [INFO] Task started: Blastn
[2024-01-25 18:59:55,026] [INFO] Running command: blastn -query GCF_000178335.1_ASM17833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/reference_markers.fasta -out GCF_000178335.1_ASM17833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:55,564] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:55,566] [INFO] Selected 9 target genomes.
[2024-01-25 18:59:55,567] [INFO] Target genome list was writen to GCF_000178335.1_ASM17833v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:55,577] [INFO] Task started: fastANI
[2024-01-25 18:59:55,577] [INFO] Running command: fastANI --query /var/lib/cwl/stga643504a-db18-414c-bef6-a11f62af17fe/GCF_000178335.1_ASM17833v1_genomic.fna.gz --refList GCF_000178335.1_ASM17833v1_genomic.fna/target_genomes.txt --output GCF_000178335.1_ASM17833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:58,887] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:58,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:58,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:58,893] [INFO] Found 4 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:59:58,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:58,893] [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
Fannyhessea vaginae	strain=DSM 15829	GCA_000178335.1	82135	82135	type	True	100.0	444	445	95	conclusive
Fannyhessea vaginae	strain=DSM 15829	GCA_000159235.2	82135	82135	type	True	99.9896	440	445	95	conclusive
Fannyhessea vaginae	strain=NCTC13935	GCA_900445305.1	82135	82135	type	True	99.9885	445	445	95	conclusive
Fannyhessea vaginae	strain=FDAARGOS_934	GCA_016026575.1	82135	82135	type	True	99.984	445	445	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:59:58,894] [INFO] DFAST Taxonomy check result was written to GCF_000178335.1_ASM17833v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:58,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:58,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:58,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/checkm_data
[2024-01-25 18:59:58,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:58,913] [INFO] Task started: CheckM
[2024-01-25 18:59:58,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178335.1_ASM17833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178335.1_ASM17833v1_genomic.fna/checkm_input GCF_000178335.1_ASM17833v1_genomic.fna/checkm_result
[2024-01-25 19:00:13,760] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:13,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:13,780] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:13,781] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:13,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178335.1_ASM17833v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:13,781] [INFO] Task started: Blastn
[2024-01-25 19:00:13,781] [INFO] Running command: blastn -query GCF_000178335.1_ASM17833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b9a6c26-4cb6-4ad7-916a-5a646f34d760/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178335.1_ASM17833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:14,564] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:14,568] [INFO] Selected 19 target genomes.
[2024-01-25 19:00:14,568] [INFO] Target genome list was writen to GCF_000178335.1_ASM17833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:14,587] [INFO] Task started: fastANI
[2024-01-25 19:00:14,587] [INFO] Running command: fastANI --query /var/lib/cwl/stga643504a-db18-414c-bef6-a11f62af17fe/GCF_000178335.1_ASM17833v1_genomic.fna.gz --refList GCF_000178335.1_ASM17833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000178335.1_ASM17833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:20,960] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:20,963] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:20,964] [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_000159235.2	s__Fannyhessea vaginae	99.9896	440	445	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Fannyhessea	95.0	98.56	95.72	0.97	0.92	6	conclusive
GCF_900343135.1	s__Fannyhessea massiliense	79.5725	106	445	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Fannyhessea	95.0	96.69	96.69	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:20,965] [INFO] GTDB search result was written to GCF_000178335.1_ASM17833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:20,967] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:20,970] [INFO] DFAST_QC result json was written to GCF_000178335.1_ASM17833v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:20,970] [INFO] DFAST_QC completed!
[2024-01-25 19:00:20,970] [INFO] Total running time: 0h0m30s