[2024-01-24 13:22:55,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference
[2024-01-24 13:22:56,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,747] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgb23690e9-6366-4d25-882e-2b30dc6e9bbc/GCF_019891355.1_ASM1989135v1_genomic.fna.gz | prodigal -d GCF_019891355.1_ASM1989135v1_genomic.fna/cds.fna -a GCF_019891355.1_ASM1989135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:11,293] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:11,294] [INFO] Task started: HMMsearch
[2024-01-24 13:23:11,294] [INFO] Running command: hmmsearch --tblout GCF_019891355.1_ASM1989135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/reference_markers.hmm GCF_019891355.1_ASM1989135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:11,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:11,589] [INFO] Found 6/6 markers.
[2024-01-24 13:23:11,632] [INFO] Query marker FASTA was written to GCF_019891355.1_ASM1989135v1_genomic.fna/markers.fasta
[2024-01-24 13:23:11,633] [INFO] Task started: Blastn
[2024-01-24 13:23:11,633] [INFO] Running command: blastn -query GCF_019891355.1_ASM1989135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/reference_markers.fasta -out GCF_019891355.1_ASM1989135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:12,602] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:12,606] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:12,606] [INFO] Target genome list was writen to GCF_019891355.1_ASM1989135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:12,609] [INFO] Task started: fastANI
[2024-01-24 13:23:12,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23690e9-6366-4d25-882e-2b30dc6e9bbc/GCF_019891355.1_ASM1989135v1_genomic.fna.gz --refList GCF_019891355.1_ASM1989135v1_genomic.fna/target_genomes.txt --output GCF_019891355.1_ASM1989135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:24,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:24,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:24,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:24,771] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:24,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:24,771] [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
Nitratireductor aquibiodomus	strain=JCM 21793	GCA_000615975.1	204799	204799	type	True	95.2099	1182	1457	95	conclusive
Nitratireductor kimnyeongensis	strain=KACC 11904	GCA_019891395.1	430679	430679	type	True	86.5	1078	1457	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	81.4522	853	1457	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	81.3005	883	1457	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	80.9893	700	1457	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	79.3858	556	1457	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.7028	495	1457	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.0885	473	1457	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.0829	448	1457	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.9847	421	1457	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	77.8684	422	1457	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	77.4467	133	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,773] [INFO] DFAST Taxonomy check result was written to GCF_019891355.1_ASM1989135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:24,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:24,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:24,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/checkm_data
[2024-01-24 13:23:24,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:24,820] [INFO] Task started: CheckM
[2024-01-24 13:23:24,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019891355.1_ASM1989135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019891355.1_ASM1989135v1_genomic.fna/checkm_input GCF_019891355.1_ASM1989135v1_genomic.fna/checkm_result
[2024-01-24 13:24:09,361] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:09,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:09,392] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:09,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:09,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019891355.1_ASM1989135v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:09,394] [INFO] Task started: Blastn
[2024-01-24 13:24:09,394] [INFO] Running command: blastn -query GCF_019891355.1_ASM1989135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f448d7b-8e60-4772-9449-f14a7b8eb225/dqc_reference/reference_markers_gtdb.fasta -out GCF_019891355.1_ASM1989135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:11,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:11,005] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:11,006] [INFO] Target genome list was writen to GCF_019891355.1_ASM1989135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:11,062] [INFO] Task started: fastANI
[2024-01-24 13:24:11,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23690e9-6366-4d25-882e-2b30dc6e9bbc/GCF_019891355.1_ASM1989135v1_genomic.fna.gz --refList GCF_019891355.1_ASM1989135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019891355.1_ASM1989135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:22,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:22,809] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:22,810] [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_000615975.1	s__Nitratireductor aquibiodomus	95.1945	1183	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	97.24	95.23	0.87	0.84	4	conclusive
GCA_002697745.1	s__Nitratireductor sp002697745	88.5096	1079	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794765.1	s__Nitratireductor sp017794765	87.2725	1006	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255295.1	s__Nitratireductor aquimarinus	85.625	1052	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	98.42	98.07	0.93	0.92	7	-
GCF_000300335.1	s__Nitratireductor pacificus	81.4493	854	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	81.3083	882	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	80.9707	702	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	78.5331	450	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_014200015.1	s__Aminobacter niigataensis	78.144	463	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_002294985.1	s__Mesorhizobium sp002294985	78.0809	432	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	-
GCF_015158295.1	s__Devosia sp015158295	77.4467	133	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176975.1	s__Aureimonas_A psammosilene	77.1486	243	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380075.1	s__WHSO01 sp009380075	76.2608	68	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:22,811] [INFO] GTDB search result was written to GCF_019891355.1_ASM1989135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:22,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:22,815] [INFO] DFAST_QC result json was written to GCF_019891355.1_ASM1989135v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:22,816] [INFO] DFAST_QC completed!
[2024-01-24 13:24:22,816] [INFO] Total running time: 0h1m27s