[2024-01-24 13:51:10,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:10,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:10,161] [INFO] DQC Reference Directory: /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference
[2024-01-24 13:51:11,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:11,325] [INFO] Task started: Prodigal
[2024-01-24 13:51:11,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aaafe5f-9fb0-4a39-823c-737bc2133366/GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/cds.fna -a GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:34,975] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:34,975] [INFO] Task started: HMMsearch
[2024-01-24 13:51:34,976] [INFO] Running command: hmmsearch --tblout GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/reference_markers.hmm GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:35,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:35,320] [INFO] Found 6/6 markers.
[2024-01-24 13:51:35,396] [INFO] Query marker FASTA was written to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:51:35,396] [INFO] Task started: Blastn
[2024-01-24 13:51:35,396] [INFO] Running command: blastn -query GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/reference_markers.fasta -out GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:36,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:36,390] [INFO] Selected 13 target genomes.
[2024-01-24 13:51:36,391] [INFO] Target genome list was writen to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:51:36,418] [INFO] Task started: fastANI
[2024-01-24 13:51:36,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aaafe5f-9fb0-4a39-823c-737bc2133366/GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna.gz --refList GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:56,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:56,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:56,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:56,248] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:56,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:56,248] [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 lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	100.0	2595	2599	95	conclusive
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	87.4758	1658	2599	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	85.7929	1468	2599	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	85.1324	1578	2599	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	85.0447	1566	2599	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	84.7479	1533	2599	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	84.5229	1434	2599	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	84.5103	1429	2599	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	83.4299	1457	2599	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.7992	1013	2599	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.5843	1047	2599	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.9098	686	2599	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.874	871	2599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:56,250] [INFO] DFAST Taxonomy check result was written to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:51:56,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:56,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:56,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/checkm_data
[2024-01-24 13:51:56,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:56,324] [INFO] Task started: CheckM
[2024-01-24 13:51:56,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/checkm_input GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:53:02,532] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:02,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:02,552] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:02,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:02,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:53:02,553] [INFO] Task started: Blastn
[2024-01-24 13:53:02,553] [INFO] Running command: blastn -query GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfec07cee-9f3b-46bd-b6ae-59f422c4d6d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:04,512] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:04,516] [INFO] Selected 14 target genomes.
[2024-01-24 13:53:04,517] [INFO] Target genome list was writen to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:04,605] [INFO] Task started: fastANI
[2024-01-24 13:53:04,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aaafe5f-9fb0-4a39-823c-737bc2133366/GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna.gz --refList GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:27,841] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:27,859] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:27,859] [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_900094565.1	s__Rhizobium lusitanum	100.0	2595	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.73	98.48	0.89	0.84	20	conclusive
GCF_016901135.1	s__Rhizobium lusitanum_D	93.3964	1823	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745725.1	s__Rhizobium rhizogenes_B	92.6703	1855	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745735.1	s__Rhizobium rhizogenes_A	87.6285	1669	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627795.1	s__Rhizobium sp003627795	86.9434	1721	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.80	99.80	0.98	0.98	2	-
GCF_001692325.1	s__Rhizobium sp001692325	86.8475	1582	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.36	95.29	0.93	0.90	3	-
GCA_900469615.1	s__Rhizobium sp900469615	85.5135	1421	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.94	98.72	0.95	0.92	12	-
GCF_008370325.1	s__Rhizobium tropici_B	85.3987	1539	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094585.1	s__Rhizobium multihospitium	85.1272	1579	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.86	97.86	0.88	0.88	2	-
GCF_900094555.1	s__Rhizobium hainanense	85.0415	1567	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472485.1	s__Rhizobium sp900472485	84.9096	1519	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.96	99.92	0.99	0.98	3	-
GCF_000696095.1	s__Rhizobium rhizogenes	84.5271	1433	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.11	97.39	0.91	0.86	92	-
GCF_009498525.1	s__Rhizobium sp009498525	84.5152	1457	2599	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	84.4861	1450	2599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:27,863] [INFO] GTDB search result was written to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:27,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:27,868] [INFO] DFAST_QC result json was written to GCF_900094565.1_IMG-taxon_2615840626_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:53:27,868] [INFO] DFAST_QC completed!
[2024-01-24 13:53:27,868] [INFO] Total running time: 0h2m18s