[2024-01-25 20:03:35,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference
[2024-01-25 20:03:36,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,660] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ce4768c-a1ad-4e20-8050-b6a8fb85ddd7/GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/cds.fna -a GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:44,221] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:44,221] [INFO] Task started: HMMsearch
[2024-01-25 20:03:44,221] [INFO] Running command: hmmsearch --tblout GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/reference_markers.hmm GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:44,459] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:44,459] [INFO] Found 6/6 markers.
[2024-01-25 20:03:44,484] [INFO] Query marker FASTA was written to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:03:44,485] [INFO] Task started: Blastn
[2024-01-25 20:03:44,485] [INFO] Running command: blastn -query GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/reference_markers.fasta -out GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:45,038] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:45,041] [INFO] Selected 13 target genomes.
[2024-01-25 20:03:45,041] [INFO] Target genome list was writen to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:03:45,051] [INFO] Task started: fastANI
[2024-01-25 20:03:45,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ce4768c-a1ad-4e20-8050-b6a8fb85ddd7/GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna.gz --refList GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:53,976] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:53,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:53,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:53,983] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:53,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:53,983] [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
Bhargavaea beijingensis	strain=CGMCC 1.6762	GCA_900101985.1	426756	426756	type	True	100.0	970	973	95	conclusive
Bhargavaea massiliensis	strain=Marseille-Q1000	GCA_018390575.1	2697500	2697500	type	True	89.0289	831	973	95	below_threshold
Bhargavaea cecembensis	strain=DSE10	GCA_000348905.1	394098	394098	type	True	85.6291	764	973	95	below_threshold
Bhargavaea ginsengi	strain=CGMCC 1.6763	GCA_900109165.1	426757	426757	type	True	83.2498	734	973	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	75.9341	66	973	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_004761885.1	1373	1373	type	True	75.755	58	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:53,985] [INFO] DFAST Taxonomy check result was written to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:03:53,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:53,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:53,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/checkm_data
[2024-01-25 20:03:53,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:54,019] [INFO] Task started: CheckM
[2024-01-25 20:03:54,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/checkm_input GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:04:21,061] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:21,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:21,111] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:21,111] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:21,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:04:21,113] [INFO] Task started: Blastn
[2024-01-25 20:04:21,113] [INFO] Running command: blastn -query GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e1c8210-8b6a-43e9-9e07-24bb618769be/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:21,907] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:21,910] [INFO] Selected 5 target genomes.
[2024-01-25 20:04:21,910] [INFO] Target genome list was writen to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:21,917] [INFO] Task started: fastANI
[2024-01-25 20:04:21,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ce4768c-a1ad-4e20-8050-b6a8fb85ddd7/GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna.gz --refList GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:25,719] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:25,724] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:25,724] [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_900101985.1	s__Bhargavaea beijingensis	100.0	970	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	99.27	99.27	0.96	0.96	2	conclusive
GCF_018390575.1	s__Bhargavaea sp018390575	89.0306	831	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348905.1	s__Bhargavaea cecembensis	85.6291	764	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009761675.1	s__Bhargavaea sp009761675	84.789	787	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001619585.1	s__Bhargavaea cecembensis_A	84.6355	765	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:25,726] [INFO] GTDB search result was written to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:25,726] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:25,728] [INFO] DFAST_QC result json was written to GCF_900101985.1_IMG-taxon_2619618820_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:04:25,728] [INFO] DFAST_QC completed!
[2024-01-25 20:04:25,729] [INFO] Total running time: 0h0m50s