[2024-01-25 18:00:20,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference
[2024-01-25 18:00:21,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,787] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg815dae5a-44e1-4e48-95e3-ead40299d847/GCF_003240565.2_ASM324056v2_genomic.fna.gz | prodigal -d GCF_003240565.2_ASM324056v2_genomic.fna/cds.fna -a GCF_003240565.2_ASM324056v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:37,984] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:37,985] [INFO] Task started: HMMsearch
[2024-01-25 18:00:37,985] [INFO] Running command: hmmsearch --tblout GCF_003240565.2_ASM324056v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/reference_markers.hmm GCF_003240565.2_ASM324056v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:38,233] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:38,234] [INFO] Found 6/6 markers.
[2024-01-25 18:00:38,279] [INFO] Query marker FASTA was written to GCF_003240565.2_ASM324056v2_genomic.fna/markers.fasta
[2024-01-25 18:00:38,279] [INFO] Task started: Blastn
[2024-01-25 18:00:38,279] [INFO] Running command: blastn -query GCF_003240565.2_ASM324056v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/reference_markers.fasta -out GCF_003240565.2_ASM324056v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:39,193] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:39,196] [INFO] Selected 27 target genomes.
[2024-01-25 18:00:39,196] [INFO] Target genome list was writen to GCF_003240565.2_ASM324056v2_genomic.fna/target_genomes.txt
[2024-01-25 18:00:39,208] [INFO] Task started: fastANI
[2024-01-25 18:00:39,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg815dae5a-44e1-4e48-95e3-ead40299d847/GCF_003240565.2_ASM324056v2_genomic.fna.gz --refList GCF_003240565.2_ASM324056v2_genomic.fna/target_genomes.txt --output GCF_003240565.2_ASM324056v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:14,488] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:14,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:14,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:14,504] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:14,504] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:14,504] [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
Rhizobium tumorigenes	strain=1078	GCA_003240565.1	2041385	2041385	type	True	99.9443	1913	1990	95	conclusive
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	80.08	850	1990	95	below_threshold
Rhizobium tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	80.05	847	1990	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	80.0322	862	1990	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.7128	762	1990	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	79.7031	787	1990	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	79.6601	729	1990	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.5763	749	1990	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	79.5242	815	1990	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	79.4879	822	1990	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	79.4847	724	1990	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	79.4813	824	1990	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	79.4755	818	1990	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	79.4323	786	1990	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	79.4095	826	1990	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	79.3115	815	1990	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	79.2833	820	1990	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	79.0963	595	1990	95	below_threshold
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	78.999	644	1990	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.9947	621	1990	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.7898	573	1990	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	78.6411	500	1990	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	78.5707	583	1990	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	78.5188	492	1990	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.51	538	1990	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4121	508	1990	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.4024	524	1990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:14,505] [INFO] DFAST Taxonomy check result was written to GCF_003240565.2_ASM324056v2_genomic.fna/tc_result.tsv
[2024-01-25 18:01:14,506] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:14,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:14,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/checkm_data
[2024-01-25 18:01:14,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:14,563] [INFO] Task started: CheckM
[2024-01-25 18:01:14,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003240565.2_ASM324056v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003240565.2_ASM324056v2_genomic.fna/checkm_input GCF_003240565.2_ASM324056v2_genomic.fna/checkm_result
[2024-01-25 18:02:00,466] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:00,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:00,485] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:00,485] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:00,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003240565.2_ASM324056v2_genomic.fna/markers.fasta)
[2024-01-25 18:02:00,486] [INFO] Task started: Blastn
[2024-01-25 18:02:00,486] [INFO] Running command: blastn -query GCF_003240565.2_ASM324056v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ac4c60-5758-498e-bb04-0a0df8e400b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003240565.2_ASM324056v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:02,322] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:02,325] [INFO] Selected 22 target genomes.
[2024-01-25 18:02:02,326] [INFO] Target genome list was writen to GCF_003240565.2_ASM324056v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:02,374] [INFO] Task started: fastANI
[2024-01-25 18:02:02,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg815dae5a-44e1-4e48-95e3-ead40299d847/GCF_003240565.2_ASM324056v2_genomic.fna.gz --refList GCF_003240565.2_ASM324056v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003240565.2_ASM324056v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:30,214] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:30,227] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:30,227] [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_003240565.1	s__Rhizobium tumorigenes	99.9443	1913	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.15	97.15	0.93	0.93	2	conclusive
GCF_007000325.1	s__Rhizobium sp007000325	93.7445	1553	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.07	97.10	0.92	0.88	7	-
GCF_014195095.1	s__Rhizobium sp014195095	80.1464	877	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003240585.1	s__Rhizobium tubonense	80.06	845	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864575.1	s__Rhizobium sp900468685	79.9754	786	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.95	0.90	0.89	5	-
GCA_900470805.1	s__Rhizobium sp900470805	79.9368	738	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472625.1	s__Rhizobium sp900472625	79.8975	774	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	79.7434	824	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_002531825.1	s__Rhizobium sp002531825	79.735	774	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900465675.1	s__Rhizobium sp900465675	79.7319	745	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	96.80	0.93	0.89	7	-
GCA_900471515.1	s__Rhizobium sp900471515	79.7211	719	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	79.6171	813	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_004341625.1	s__Rhizobium sp004341625	79.6131	834	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_002008365.1	s__Rhizobium leguminosarum	79.4752	825	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	-
GCF_017873135.1	s__Pararhizobium herbae	79.3588	669	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094555.1	s__Rhizobium hainanense	79.3229	813	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900468805.1	s__Rhizobium sp900468805	79.1662	727	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.10	98.22	0.94	0.90	7	-
GCF_000298315.2	s__Rhizobium grahamii	79.0961	595	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.32	97.32	0.91	0.91	2	-
GCA_900472175.1	s__Pararhizobium sp900472175	79.073	566	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424945.1	s__Rhizobium sp001424945	79.0696	645	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.84	96.05	0.91	0.86	3	-
GCF_000745575.1	s__Pararhizobium sp000745575	79.0462	615	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	96.55	96.55	0.93	0.93	2	-
GCA_900466605.1	s__Rhizobium sp900466605	78.7482	564	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:30,229] [INFO] GTDB search result was written to GCF_003240565.2_ASM324056v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:30,229] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:30,233] [INFO] DFAST_QC result json was written to GCF_003240565.2_ASM324056v2_genomic.fna/dqc_result.json
[2024-01-25 18:02:30,233] [INFO] DFAST_QC completed!
[2024-01-25 18:02:30,233] [INFO] Total running time: 0h2m10s