[2024-01-24 13:37:39,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:39,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:39,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference
[2024-01-24 13:37:41,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:41,039] [INFO] Task started: Prodigal
[2024-01-24 13:37:41,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb5d06ba-d526-4f8e-adf3-ea0daeb4a085/GCF_021654575.1_ASM2165457v1_genomic.fna.gz | prodigal -d GCF_021654575.1_ASM2165457v1_genomic.fna/cds.fna -a GCF_021654575.1_ASM2165457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:38:01,983] [INFO] Task succeeded: Prodigal
[2024-01-24 13:38:01,983] [INFO] Task started: HMMsearch
[2024-01-24 13:38:01,983] [INFO] Running command: hmmsearch --tblout GCF_021654575.1_ASM2165457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/reference_markers.hmm GCF_021654575.1_ASM2165457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:38:02,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:38:02,367] [INFO] Found 6/6 markers.
[2024-01-24 13:38:02,409] [INFO] Query marker FASTA was written to GCF_021654575.1_ASM2165457v1_genomic.fna/markers.fasta
[2024-01-24 13:38:02,409] [INFO] Task started: Blastn
[2024-01-24 13:38:02,409] [INFO] Running command: blastn -query GCF_021654575.1_ASM2165457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/reference_markers.fasta -out GCF_021654575.1_ASM2165457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:02,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:02,981] [INFO] Selected 31 target genomes.
[2024-01-24 13:38:02,981] [INFO] Target genome list was writen to GCF_021654575.1_ASM2165457v1_genomic.fna/target_genomes.txt
[2024-01-24 13:38:03,002] [INFO] Task started: fastANI
[2024-01-24 13:38:03,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5d06ba-d526-4f8e-adf3-ea0daeb4a085/GCF_021654575.1_ASM2165457v1_genomic.fna.gz --refList GCF_021654575.1_ASM2165457v1_genomic.fna/target_genomes.txt --output GCF_021654575.1_ASM2165457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:29,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:29,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:29,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:29,317] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:38:29,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:38:29,317] [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
Desulfoluna spongiiphila	strain=AA1	GCA_900101345.1	419481	419481	type	True	81.6813	1171	2087	95	below_threshold
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	76.2309	68	2087	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.0354	81	2087	95	below_threshold
Desulfobotulus alkaliphilus	strain=ASO4-4	GCA_007830435.1	622671	622671	type	True	75.7233	69	2087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:29,318] [INFO] DFAST Taxonomy check result was written to GCF_021654575.1_ASM2165457v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:29,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:29,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:29,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/checkm_data
[2024-01-24 13:38:29,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:29,377] [INFO] Task started: CheckM
[2024-01-24 13:38:29,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654575.1_ASM2165457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654575.1_ASM2165457v1_genomic.fna/checkm_input GCF_021654575.1_ASM2165457v1_genomic.fna/checkm_result
[2024-01-24 13:39:28,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:28,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:28,387] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:28,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:28,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654575.1_ASM2165457v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:28,387] [INFO] Task started: Blastn
[2024-01-24 13:39:28,387] [INFO] Running command: blastn -query GCF_021654575.1_ASM2165457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d119709-c90f-446d-8e76-3cc04463ad09/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654575.1_ASM2165457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:29,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:29,172] [INFO] Selected 21 target genomes.
[2024-01-24 13:39:29,172] [INFO] Target genome list was writen to GCF_021654575.1_ASM2165457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:29,193] [INFO] Task started: fastANI
[2024-01-24 13:39:29,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5d06ba-d526-4f8e-adf3-ea0daeb4a085/GCF_021654575.1_ASM2165457v1_genomic.fna.gz --refList GCF_021654575.1_ASM2165457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654575.1_ASM2165457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:46,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:46,590] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:39:46,590] [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_900101345.1	s__Desulfoluna spongiiphila	81.661	1173	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfolunaceae;g__Desulfoluna	95.0	98.60	98.60	0.95	0.95	2	-
GCF_900699765.1	s__Desulfoluna butyratoxydans	81.2829	1117	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfolunaceae;g__Desulfoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619155.1	s__Desulfoluna sp013619155	79.8773	694	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfolunaceae;g__Desulfoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851005.1	s__Desulfonema_B ishimotonii	76.3365	69	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfonema_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	76.0361	81	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830435.1	s__Desulfobotulus alkaliphilus	75.6694	69	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulforegulaceae;g__Desulfobotulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342285.1	s__JAEINQ01 sp016342285	75.6496	78	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224455.1	s__Desulfosarcina sp018224455	75.6272	55	2087	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:46,591] [INFO] GTDB search result was written to GCF_021654575.1_ASM2165457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:46,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:46,594] [INFO] DFAST_QC result json was written to GCF_021654575.1_ASM2165457v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:46,594] [INFO] DFAST_QC completed!
[2024-01-24 13:39:46,594] [INFO] Total running time: 0h2m7s