[2023-06-27 03:44:49,346] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:44:49,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:44:49,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference
[2023-06-27 03:44:50,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:44:50,755] [INFO] Task started: Prodigal
[2023-06-27 03:44:50,755] [INFO] Running command: gunzip -c /var/lib/cwl/stga581a03e-5a22-47b3-8ab2-ccd024385282/GCA_026417795.1_ASM2641779v1_genomic.fna.gz | prodigal -d GCA_026417795.1_ASM2641779v1_genomic.fna/cds.fna -a GCA_026417795.1_ASM2641779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:44:56,263] [INFO] Task succeeded: Prodigal
[2023-06-27 03:44:56,263] [INFO] Task started: HMMsearch
[2023-06-27 03:44:56,263] [INFO] Running command: hmmsearch --tblout GCA_026417795.1_ASM2641779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/reference_markers.hmm GCA_026417795.1_ASM2641779v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:44:56,504] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:44:56,505] [INFO] Found 6/6 markers.
[2023-06-27 03:44:56,541] [INFO] Query marker FASTA was written to GCA_026417795.1_ASM2641779v1_genomic.fna/markers.fasta
[2023-06-27 03:44:56,541] [INFO] Task started: Blastn
[2023-06-27 03:44:56,541] [INFO] Running command: blastn -query GCA_026417795.1_ASM2641779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/reference_markers.fasta -out GCA_026417795.1_ASM2641779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:44:57,150] [INFO] Task succeeded: Blastn
[2023-06-27 03:44:57,154] [INFO] Selected 14 target genomes.
[2023-06-27 03:44:57,155] [INFO] Target genome list was writen to GCA_026417795.1_ASM2641779v1_genomic.fna/target_genomes.txt
[2023-06-27 03:44:57,158] [INFO] Task started: fastANI
[2023-06-27 03:44:57,158] [INFO] Running command: fastANI --query /var/lib/cwl/stga581a03e-5a22-47b3-8ab2-ccd024385282/GCA_026417795.1_ASM2641779v1_genomic.fna.gz --refList GCA_026417795.1_ASM2641779v1_genomic.fna/target_genomes.txt --output GCA_026417795.1_ASM2641779v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:45:04,062] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:04,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:45:04,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:45:04,072] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:45:04,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:45:04,072] [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
Thermanaerovibrio velox	strain=DSM 12556	GCA_000237825.1	108007	108007	type	True	85.2271	513	576	95	below_threshold
Thermanaerovibrio acidaminovorans	strain=DSM 6589	GCA_000024905.1	81462	81462	type	True	81.0149	348	576	95	below_threshold
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	77.8592	181	576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:45:04,074] [INFO] DFAST Taxonomy check result was written to GCA_026417795.1_ASM2641779v1_genomic.fna/tc_result.tsv
[2023-06-27 03:45:04,075] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:45:04,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:45:04,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/checkm_data
[2023-06-27 03:45:04,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:45:04,102] [INFO] Task started: CheckM
[2023-06-27 03:45:04,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026417795.1_ASM2641779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026417795.1_ASM2641779v1_genomic.fna/checkm_input GCA_026417795.1_ASM2641779v1_genomic.fna/checkm_result
[2023-06-27 03:45:27,005] [INFO] Task succeeded: CheckM
[2023-06-27 03:45:27,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.69%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:45:27,027] [INFO] ===== Completeness check finished =====
[2023-06-27 03:45:27,028] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:45:27,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026417795.1_ASM2641779v1_genomic.fna/markers.fasta)
[2023-06-27 03:45:27,028] [INFO] Task started: Blastn
[2023-06-27 03:45:27,029] [INFO] Running command: blastn -query GCA_026417795.1_ASM2641779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aa469ff-671e-4042-ac6c-15b9cbd3921f/dqc_reference/reference_markers_gtdb.fasta -out GCA_026417795.1_ASM2641779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:45:27,830] [INFO] Task succeeded: Blastn
[2023-06-27 03:45:27,835] [INFO] Selected 14 target genomes.
[2023-06-27 03:45:27,835] [INFO] Target genome list was writen to GCA_026417795.1_ASM2641779v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:45:27,871] [INFO] Task started: fastANI
[2023-06-27 03:45:27,872] [INFO] Running command: fastANI --query /var/lib/cwl/stga581a03e-5a22-47b3-8ab2-ccd024385282/GCA_026417795.1_ASM2641779v1_genomic.fna.gz --refList GCA_026417795.1_ASM2641779v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026417795.1_ASM2641779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:45:33,270] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:33,279] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 03:45:33,279] [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_000237825.1	s__Thermanaerovibrio velox	85.2255	512	576	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Thermanaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024905.1	s__Thermanaerovibrio acidaminovorans	80.985	349	576	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Thermanaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165795.1	s__Aminomonas paucivorans	77.8342	183	576	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Aminomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:45:33,282] [INFO] GTDB search result was written to GCA_026417795.1_ASM2641779v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:45:33,282] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:45:33,285] [INFO] DFAST_QC result json was written to GCA_026417795.1_ASM2641779v1_genomic.fna/dqc_result.json
[2023-06-27 03:45:33,285] [INFO] DFAST_QC completed!
[2023-06-27 03:45:33,285] [INFO] Total running time: 0h0m44s