[2024-01-24 13:45:42,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:42,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:42,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference
[2024-01-24 13:45:43,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:43,651] [INFO] Task started: Prodigal
[2024-01-24 13:45:43,651] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6baece5-07a3-477e-995e-1f0288d90ce3/GCF_009617855.1_ASM961785v1_genomic.fna.gz | prodigal -d GCF_009617855.1_ASM961785v1_genomic.fna/cds.fna -a GCF_009617855.1_ASM961785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:09,199] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:09,199] [INFO] Task started: HMMsearch
[2024-01-24 13:46:09,200] [INFO] Running command: hmmsearch --tblout GCF_009617855.1_ASM961785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/reference_markers.hmm GCF_009617855.1_ASM961785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:09,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:09,564] [INFO] Found 6/6 markers.
[2024-01-24 13:46:09,606] [INFO] Query marker FASTA was written to GCF_009617855.1_ASM961785v1_genomic.fna/markers.fasta
[2024-01-24 13:46:09,607] [INFO] Task started: Blastn
[2024-01-24 13:46:09,607] [INFO] Running command: blastn -query GCF_009617855.1_ASM961785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/reference_markers.fasta -out GCF_009617855.1_ASM961785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:10,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:10,268] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:10,269] [INFO] Target genome list was writen to GCF_009617855.1_ASM961785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:10,277] [INFO] Task started: fastANI
[2024-01-24 13:46:10,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6baece5-07a3-477e-995e-1f0288d90ce3/GCF_009617855.1_ASM961785v1_genomic.fna.gz --refList GCF_009617855.1_ASM961785v1_genomic.fna/target_genomes.txt --output GCF_009617855.1_ASM961785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:18,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:18,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:18,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:18,658] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:18,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:18,659] [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
Prolixibacter denitrificans	strain=MIC1-1	GCA_009617855.1	1541063	1541063	type	True	100.0	1589	1589	95	conclusive
Prolixibacter denitrificans	strain=DSM 27267	GCA_003014495.1	1541063	1541063	type	True	99.9788	1558	1589	95	conclusive
Prolixibacter bellariivorans	strain=JCM 13498	GCA_009617915.1	314319	314319	type	True	85.3971	1258	1589	95	below_threshold
Prolixibacter bellariivorans	strain=ATCC BAA-1284	GCA_000621705.1	314319	314319	type	True	85.3638	1259	1589	95	below_threshold
Prolixibacter bellariivorans	strain=JCM 13498	GCA_000614865.1	314319	314319	type	True	85.2645	1259	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:18,661] [INFO] DFAST Taxonomy check result was written to GCF_009617855.1_ASM961785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:18,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:18,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:18,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/checkm_data
[2024-01-24 13:46:18,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:18,711] [INFO] Task started: CheckM
[2024-01-24 13:46:18,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009617855.1_ASM961785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009617855.1_ASM961785v1_genomic.fna/checkm_input GCF_009617855.1_ASM961785v1_genomic.fna/checkm_result
[2024-01-24 13:47:31,550] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:31,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:31,570] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:31,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:31,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009617855.1_ASM961785v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:31,571] [INFO] Task started: Blastn
[2024-01-24 13:47:31,571] [INFO] Running command: blastn -query GCF_009617855.1_ASM961785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da62438-857b-447f-b729-0a8f94201478/dqc_reference/reference_markers_gtdb.fasta -out GCF_009617855.1_ASM961785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:32,503] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:32,508] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:32,508] [INFO] Target genome list was writen to GCF_009617855.1_ASM961785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:32,530] [INFO] Task started: fastANI
[2024-01-24 13:47:32,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6baece5-07a3-477e-995e-1f0288d90ce3/GCF_009617855.1_ASM961785v1_genomic.fna.gz --refList GCF_009617855.1_ASM961785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009617855.1_ASM961785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:41,691] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,702] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:41,702] [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_003014495.1	s__Prolixibacter denitrificans	99.9788	1558	1589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009617875.1	s__Prolixibacter sp009617875	93.3858	1372	1589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621705.1	s__Prolixibacter bellariivorans	85.3595	1259	1589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	99.99	99.97	1.00	1.00	3	-
GCF_009617895.1	s__Prolixibacter sp009617895	83.9972	984	1589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Prolixibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:41,704] [INFO] GTDB search result was written to GCF_009617855.1_ASM961785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:41,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:41,708] [INFO] DFAST_QC result json was written to GCF_009617855.1_ASM961785v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:41,708] [INFO] DFAST_QC completed!
[2024-01-24 13:47:41,708] [INFO] Total running time: 0h1m59s