[2024-01-24 13:27:25,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:25,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:25,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference
[2024-01-24 13:27:26,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:26,467] [INFO] Task started: Prodigal
[2024-01-24 13:27:26,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg86664fdd-71ac-46d0-afd5-03f66812bf0f/GCF_007002985.1_ASM700298v1_genomic.fna.gz | prodigal -d GCF_007002985.1_ASM700298v1_genomic.fna/cds.fna -a GCF_007002985.1_ASM700298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:47,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:47,135] [INFO] Task started: HMMsearch
[2024-01-24 13:27:47,135] [INFO] Running command: hmmsearch --tblout GCF_007002985.1_ASM700298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/reference_markers.hmm GCF_007002985.1_ASM700298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:47,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:47,473] [INFO] Found 6/6 markers.
[2024-01-24 13:27:47,531] [INFO] Query marker FASTA was written to GCF_007002985.1_ASM700298v1_genomic.fna/markers.fasta
[2024-01-24 13:27:47,532] [INFO] Task started: Blastn
[2024-01-24 13:27:47,532] [INFO] Running command: blastn -query GCF_007002985.1_ASM700298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/reference_markers.fasta -out GCF_007002985.1_ASM700298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:48,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:48,544] [INFO] Selected 15 target genomes.
[2024-01-24 13:27:48,545] [INFO] Target genome list was writen to GCF_007002985.1_ASM700298v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:48,556] [INFO] Task started: fastANI
[2024-01-24 13:27:48,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg86664fdd-71ac-46d0-afd5-03f66812bf0f/GCF_007002985.1_ASM700298v1_genomic.fna.gz --refList GCF_007002985.1_ASM700298v1_genomic.fna/target_genomes.txt --output GCF_007002985.1_ASM700298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:11,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:11,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:11,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:11,677] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:11,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:11,678] [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
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	100.0	2317	2322	95	conclusive
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	99.9946	2303	2322	95	conclusive
Rhizobium leucaenae	strain=CFN 299	GCA_014727215.1	29450	29450	type	True	84.9566	1306	2322	95	below_threshold
Rhizobium leucaenae	strain=USDA 9039	GCA_000426285.1	29450	29450	type	True	84.9132	1310	2322	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	84.9128	1380	2322	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	84.508	1440	2322	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	83.5725	1265	2322	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	83.479	1374	2322	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	83.4758	1268	2322	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	83.3848	1302	2322	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	83.1991	1362	2322	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.0241	1023	2322	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.9112	1053	2322	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.8754	928	2322	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.6684	690	2322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:11,679] [INFO] DFAST Taxonomy check result was written to GCF_007002985.1_ASM700298v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:11,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:11,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:11,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/checkm_data
[2024-01-24 13:28:11,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:11,743] [INFO] Task started: CheckM
[2024-01-24 13:28:11,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007002985.1_ASM700298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007002985.1_ASM700298v1_genomic.fna/checkm_input GCF_007002985.1_ASM700298v1_genomic.fna/checkm_result
[2024-01-24 13:29:13,067] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:13,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:13,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:13,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:13,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007002985.1_ASM700298v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:13,097] [INFO] Task started: Blastn
[2024-01-24 13:29:13,097] [INFO] Running command: blastn -query GCF_007002985.1_ASM700298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg778d8547-262e-4f66-8528-3b413accfe31/dqc_reference/reference_markers_gtdb.fasta -out GCF_007002985.1_ASM700298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:15,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:15,173] [INFO] Selected 6 target genomes.
[2024-01-24 13:29:15,173] [INFO] Target genome list was writen to GCF_007002985.1_ASM700298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:15,178] [INFO] Task started: fastANI
[2024-01-24 13:29:15,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg86664fdd-71ac-46d0-afd5-03f66812bf0f/GCF_007002985.1_ASM700298v1_genomic.fna.gz --refList GCF_007002985.1_ASM700298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007002985.1_ASM700298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:27,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:27,118] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:27,119] [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_000696095.1	s__Rhizobium rhizogenes	99.9946	2303	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.11	97.39	0.91	0.86	92	conclusive
GCF_009498525.1	s__Rhizobium sp009498525	92.3332	1916	2322	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	91.3472	1760	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189535.1	s__Rhizobium lusitanum_C	91.2462	1778	2322	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	86.7694	1628	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094565.1	s__Rhizobium lusitanum	84.4834	1444	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.73	98.48	0.89	0.84	20	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,120] [INFO] GTDB search result was written to GCF_007002985.1_ASM700298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:27,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:27,124] [INFO] DFAST_QC result json was written to GCF_007002985.1_ASM700298v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:27,125] [INFO] DFAST_QC completed!
[2024-01-24 13:29:27,125] [INFO] Total running time: 0h2m2s