[2024-01-24 13:09:30,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:30,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:30,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference
[2024-01-24 13:09:31,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:31,585] [INFO] Task started: Prodigal
[2024-01-24 13:09:31,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e2ee785-aafe-4a4a-9c20-b76bd6392bc6/GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/cds.fna -a GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:49,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:49,496] [INFO] Task started: HMMsearch
[2024-01-24 13:09:49,496] [INFO] Running command: hmmsearch --tblout GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/reference_markers.hmm GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:49,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:49,726] [INFO] Found 6/6 markers.
[2024-01-24 13:09:49,752] [INFO] Query marker FASTA was written to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:49,753] [INFO] Task started: Blastn
[2024-01-24 13:09:49,753] [INFO] Running command: blastn -query GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/reference_markers.fasta -out GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:50,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:50,355] [INFO] Selected 22 target genomes.
[2024-01-24 13:09:50,356] [INFO] Target genome list was writen to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:50,364] [INFO] Task started: fastANI
[2024-01-24 13:09:50,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e2ee785-aafe-4a4a-9c20-b76bd6392bc6/GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna.gz --refList GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:06,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:06,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:06,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:06,960] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:06,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:06,961] [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
Thermoflavifilum thermophilum	strain=DSM 14807	GCA_900116565.1	1393122	1393122	type	True	100.0	952	952	95	conclusive
Thermoflavifilum aggregans	strain=DSM 27268	GCA_002797735.1	454188	454188	type	True	89.9978	827	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:06,962] [INFO] DFAST Taxonomy check result was written to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:06,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:06,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:06,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/checkm_data
[2024-01-24 13:10:06,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:06,993] [INFO] Task started: CheckM
[2024-01-24 13:10:06,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/checkm_input GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:56,543] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:56,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:56,561] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:56,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:56,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:56,562] [INFO] Task started: Blastn
[2024-01-24 13:10:56,562] [INFO] Running command: blastn -query GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d5e224d-f427-48f4-b7ac-5d5151f33df9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:57,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:57,347] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:57,347] [INFO] Target genome list was writen to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:57,358] [INFO] Task started: fastANI
[2024-01-24 13:10:57,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e2ee785-aafe-4a4a-9c20-b76bd6392bc6/GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna.gz --refList GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:09,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:09,405] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:09,405] [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_900116565.1	s__Thermoflavifilum thermophilum	100.0	952	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002797735.1	s__Thermoflavifilum aggregans	89.9978	827	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014961315.1	s__Thermoflavifilum sp014961315	80.3764	668	952	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Thermoflavifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:09,407] [INFO] GTDB search result was written to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:09,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:09,410] [INFO] DFAST_QC result json was written to GCF_900116565.1_IMG-taxon_2600255258_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:09,410] [INFO] DFAST_QC completed!
[2024-01-24 13:11:09,410] [INFO] Total running time: 0h1m39s