[2024-01-24 13:40:46,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference
[2024-01-24 13:40:47,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,326] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,326] [INFO] Running command: gunzip -c /var/lib/cwl/stgb37fd4aa-de9f-42c4-9746-8200f00d9212/GCF_003258805.1_ASM325880v1_genomic.fna.gz | prodigal -d GCF_003258805.1_ASM325880v1_genomic.fna/cds.fna -a GCF_003258805.1_ASM325880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:02,213] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:02,213] [INFO] Task started: HMMsearch
[2024-01-24 13:41:02,214] [INFO] Running command: hmmsearch --tblout GCF_003258805.1_ASM325880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/reference_markers.hmm GCF_003258805.1_ASM325880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,537] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,591] [INFO] Query marker FASTA was written to GCF_003258805.1_ASM325880v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,592] [INFO] Task started: Blastn
[2024-01-24 13:41:02,592] [INFO] Running command: blastn -query GCF_003258805.1_ASM325880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/reference_markers.fasta -out GCF_003258805.1_ASM325880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,746] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,752] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:03,752] [INFO] Target genome list was writen to GCF_003258805.1_ASM325880v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,780] [INFO] Task started: fastANI
[2024-01-24 13:41:03,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgb37fd4aa-de9f-42c4-9746-8200f00d9212/GCF_003258805.1_ASM325880v1_genomic.fna.gz --refList GCF_003258805.1_ASM325880v1_genomic.fna/target_genomes.txt --output GCF_003258805.1_ASM325880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,771] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:22,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:22,772] [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
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	100.0	1649	1671	95	conclusive
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	99.8862	1607	1671	95	conclusive
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	86.6959	1160	1671	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	84.6837	937	1671	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	78.4699	550	1671	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	78.0398	492	1671	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	78.0349	536	1671	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.973	521	1671	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	77.9362	541	1671	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.9326	568	1671	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.925	515	1671	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.4019	432	1671	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.2574	571	1671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,773] [INFO] DFAST Taxonomy check result was written to GCF_003258805.1_ASM325880v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/checkm_data
[2024-01-24 13:41:22,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:22,845] [INFO] Task started: CheckM
[2024-01-24 13:41:22,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258805.1_ASM325880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258805.1_ASM325880v1_genomic.fna/checkm_input GCF_003258805.1_ASM325880v1_genomic.fna/checkm_result
[2024-01-24 13:42:08,148] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:08,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,173] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:08,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:08,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258805.1_ASM325880v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:08,174] [INFO] Task started: Blastn
[2024-01-24 13:42:08,174] [INFO] Running command: blastn -query GCF_003258805.1_ASM325880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a986746-0013-4673-b2e4-6a27ba1b5eb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258805.1_ASM325880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,563] [INFO] Selected 5 target genomes.
[2024-01-24 13:42:10,563] [INFO] Target genome list was writen to GCF_003258805.1_ASM325880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,589] [INFO] Task started: fastANI
[2024-01-24 13:42:10,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgb37fd4aa-de9f-42c4-9746-8200f00d9212/GCF_003258805.1_ASM325880v1_genomic.fna.gz --refList GCF_003258805.1_ASM325880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258805.1_ASM325880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:19,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:19,382] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:19,383] [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_016653355.1	s__Rhodoplanes elegans	99.8862	1607	1671	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	conclusive
GCF_003258865.1	s__Rhodoplanes roseus	86.7088	1159	1671	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	85.653	1162	1671	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	85.2232	1107	1671	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_000293785.1	s__Rhodoplanes sp000293785	82.7152	869	1671	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:19,384] [INFO] GTDB search result was written to GCF_003258805.1_ASM325880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:19,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:19,388] [INFO] DFAST_QC result json was written to GCF_003258805.1_ASM325880v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:19,388] [INFO] DFAST_QC completed!
[2024-01-24 13:42:19,388] [INFO] Total running time: 0h1m33s