[2024-01-25 19:52:35,895] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:35,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:35,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference
[2024-01-25 19:52:37,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:37,009] [INFO] Task started: Prodigal
[2024-01-25 19:52:37,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg78ccb65c-6505-44ab-9eab-7b0f60694b96/GCF_030272705.1_ASM3027270v1_genomic.fna.gz | prodigal -d GCF_030272705.1_ASM3027270v1_genomic.fna/cds.fna -a GCF_030272705.1_ASM3027270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:56,695] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:56,695] [INFO] Task started: HMMsearch
[2024-01-25 19:52:56,695] [INFO] Running command: hmmsearch --tblout GCF_030272705.1_ASM3027270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/reference_markers.hmm GCF_030272705.1_ASM3027270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:57,035] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:57,037] [INFO] Found 6/6 markers.
[2024-01-25 19:52:57,093] [INFO] Query marker FASTA was written to GCF_030272705.1_ASM3027270v1_genomic.fna/markers.fasta
[2024-01-25 19:52:57,093] [INFO] Task started: Blastn
[2024-01-25 19:52:57,093] [INFO] Running command: blastn -query GCF_030272705.1_ASM3027270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/reference_markers.fasta -out GCF_030272705.1_ASM3027270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:57,930] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:57,933] [INFO] Selected 17 target genomes.
[2024-01-25 19:52:57,933] [INFO] Target genome list was writen to GCF_030272705.1_ASM3027270v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:57,954] [INFO] Task started: fastANI
[2024-01-25 19:52:57,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ccb65c-6505-44ab-9eab-7b0f60694b96/GCF_030272705.1_ASM3027270v1_genomic.fna.gz --refList GCF_030272705.1_ASM3027270v1_genomic.fna/target_genomes.txt --output GCF_030272705.1_ASM3027270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:17,610] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:17,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:17,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:17,620] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:17,620] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:17,620] [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 jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	90.9646	1959	2394	95	below_threshold
Rhizobium leucaenae	strain=USDA 9039	GCA_000426285.1	29450	29450	type	True	87.1507	1491	2394	95	below_threshold
Rhizobium leucaenae	strain=CFN 299	GCA_014727215.1	29450	29450	type	True	87.0748	1502	2394	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	84.8934	1312	2394	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	84.8808	1321	2394	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	82.9106	1212	2394	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	82.8607	1290	2394	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	82.5704	1251	2394	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.6475	931	2394	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.4271	960	2394	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.6349	827	2394	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	78.6602	547	2394	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.7128	142	2394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:17,621] [INFO] DFAST Taxonomy check result was written to GCF_030272705.1_ASM3027270v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:17,622] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:17,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:17,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/checkm_data
[2024-01-25 19:53:17,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:17,688] [INFO] Task started: CheckM
[2024-01-25 19:53:17,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030272705.1_ASM3027270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030272705.1_ASM3027270v1_genomic.fna/checkm_input GCF_030272705.1_ASM3027270v1_genomic.fna/checkm_result
[2024-01-25 19:54:11,971] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:11,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:11,994] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:11,995] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:11,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030272705.1_ASM3027270v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:11,996] [INFO] Task started: Blastn
[2024-01-25 19:54:11,996] [INFO] Running command: blastn -query GCF_030272705.1_ASM3027270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d674156-969e-429b-8f96-5159481836eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_030272705.1_ASM3027270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:13,589] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:13,594] [INFO] Selected 18 target genomes.
[2024-01-25 19:54:13,594] [INFO] Target genome list was writen to GCF_030272705.1_ASM3027270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:13,609] [INFO] Task started: fastANI
[2024-01-25 19:54:13,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ccb65c-6505-44ab-9eab-7b0f60694b96/GCF_030272705.1_ASM3027270v1_genomic.fna.gz --refList GCF_030272705.1_ASM3027270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030272705.1_ASM3027270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:36,189] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:36,198] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:54:36,198] [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_003627755.1	s__Rhizobium jaguaris	90.9646	1959	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362445.1	s__Rhizobium sp004362445	88.559	1694	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003025035.1	s__Rhizobium paranaense	88.3388	1199	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002944315.1	s__Rhizobium sp002944315	87.6578	1604	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426285.1	s__Rhizobium leucaenae	87.1338	1493	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.87	99.71	0.96	0.93	5	-
GCF_009498525.1	s__Rhizobium sp009498525	84.9961	1308	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799715.1	s__Rhizobium rhizogenes_C	84.8936	1342	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696095.1	s__Rhizobium rhizogenes	84.8677	1322	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.11	97.39	0.91	0.86	92	-
GCF_014189535.1	s__Rhizobium lusitanum_C	84.8411	1292	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	84.7728	1302	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024605.1	s__Rhizobium sp003024605	83.1711	1015	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.03	99.00	0.96	0.95	8	-
GCF_900094555.1	s__Rhizobium hainanense	82.8827	1286	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900468625.1	s__Rhizobium sp900468625	82.831	1208	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.33	98.37	0.95	0.89	8	-
GCF_018413645.1	s__Roseococcus sp018413645	75.7312	140	2394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:36,200] [INFO] GTDB search result was written to GCF_030272705.1_ASM3027270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:36,201] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:36,203] [INFO] DFAST_QC result json was written to GCF_030272705.1_ASM3027270v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:36,203] [INFO] DFAST_QC completed!
[2024-01-25 19:54:36,203] [INFO] Total running time: 0h2m0s