[2024-01-24 12:14:48,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,708] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference
[2024-01-24 12:14:50,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,102] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9a1ca34-2e33-450c-b214-0d3a769ae552/GCF_004682015.1_ASM468201v1_genomic.fna.gz | prodigal -d GCF_004682015.1_ASM468201v1_genomic.fna/cds.fna -a GCF_004682015.1_ASM468201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:06,151] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:06,151] [INFO] Task started: HMMsearch
[2024-01-24 12:15:06,152] [INFO] Running command: hmmsearch --tblout GCF_004682015.1_ASM468201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/reference_markers.hmm GCF_004682015.1_ASM468201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:06,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:06,466] [INFO] Found 6/6 markers.
[2024-01-24 12:15:06,511] [INFO] Query marker FASTA was written to GCF_004682015.1_ASM468201v1_genomic.fna/markers.fasta
[2024-01-24 12:15:06,511] [INFO] Task started: Blastn
[2024-01-24 12:15:06,511] [INFO] Running command: blastn -query GCF_004682015.1_ASM468201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/reference_markers.fasta -out GCF_004682015.1_ASM468201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:07,676] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:07,679] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:07,680] [INFO] Target genome list was writen to GCF_004682015.1_ASM468201v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:07,688] [INFO] Task started: fastANI
[2024-01-24 12:15:07,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a1ca34-2e33-450c-b214-0d3a769ae552/GCF_004682015.1_ASM468201v1_genomic.fna.gz --refList GCF_004682015.1_ASM468201v1_genomic.fna/target_genomes.txt --output GCF_004682015.1_ASM468201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:18,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:18,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:18,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:18,538] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:18,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:18,539] [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
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	100.0	1594	1594	95	conclusive
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	84.7994	933	1594	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	83.9268	984	1594	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	83.8104	861	1594	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	83.6642	899	1594	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.4801	716	1594	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	82.0969	912	1594	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	82.0658	829	1594	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0887	662	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,545] [INFO] DFAST Taxonomy check result was written to GCF_004682015.1_ASM468201v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:18,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:18,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:18,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/checkm_data
[2024-01-24 12:15:18,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:18,613] [INFO] Task started: CheckM
[2024-01-24 12:15:18,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004682015.1_ASM468201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004682015.1_ASM468201v1_genomic.fna/checkm_input GCF_004682015.1_ASM468201v1_genomic.fna/checkm_result
[2024-01-24 12:16:25,120] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:25,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,144] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:25,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:25,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004682015.1_ASM468201v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:25,145] [INFO] Task started: Blastn
[2024-01-24 12:16:25,145] [INFO] Running command: blastn -query GCF_004682015.1_ASM468201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a3ed30-84f3-4b15-9b0e-089eb64e9f9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004682015.1_ASM468201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:27,332] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:27,336] [INFO] Selected 8 target genomes.
[2024-01-24 12:16:27,336] [INFO] Target genome list was writen to GCF_004682015.1_ASM468201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:27,345] [INFO] Task started: fastANI
[2024-01-24 12:16:27,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9a1ca34-2e33-450c-b214-0d3a769ae552/GCF_004682015.1_ASM468201v1_genomic.fna.gz --refList GCF_004682015.1_ASM468201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004682015.1_ASM468201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:36,559] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:36,572] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:36,572] [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_004682015.1	s__Ramlibacter henchirensis	100.0	1594	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424545.1	s__Ramlibacter sp001424545	87.6648	1144	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	87.0298	1088	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681975.1	s__Ramlibacter sp004681975	84.8466	929	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	83.9076	986	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000215705.1	s__Ramlibacter tataouinensis	83.8079	861	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016641735.1	s__Ramlibacter sp016641735	83.6618	899	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015159745.1	s__Ramlibacter aquaticus	82.4844	716	1594	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:36,573] [INFO] GTDB search result was written to GCF_004682015.1_ASM468201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:36,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:36,577] [INFO] DFAST_QC result json was written to GCF_004682015.1_ASM468201v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:36,577] [INFO] DFAST_QC completed!
[2024-01-24 12:16:36,577] [INFO] Total running time: 0h1m48s