[2024-01-24 14:55:07,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference
[2024-01-24 14:55:09,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,471] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgafee2e4a-cce8-4426-9edc-9e6bf02a67cc/GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/cds.fna -a GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:31,180] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:31,180] [INFO] Task started: HMMsearch
[2024-01-24 14:55:31,180] [INFO] Running command: hmmsearch --tblout GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/reference_markers.hmm GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:31,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:31,546] [INFO] Found 6/6 markers.
[2024-01-24 14:55:31,603] [INFO] Query marker FASTA was written to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:55:31,604] [INFO] Task started: Blastn
[2024-01-24 14:55:31,604] [INFO] Running command: blastn -query GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/reference_markers.fasta -out GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:32,695] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:32,698] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:32,699] [INFO] Target genome list was writen to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:55:32,709] [INFO] Task started: fastANI
[2024-01-24 14:55:32,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgafee2e4a-cce8-4426-9edc-9e6bf02a67cc/GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna.gz --refList GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:51,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:51,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:51,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:51,062] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:51,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:51,062] [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 multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	100.0	2431	2432	95	conclusive
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	91.2489	1894	2432	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	90.4093	2026	2432	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	89.1047	1684	2432	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	86.4368	1546	2432	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	86.0668	1588	2432	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	83.3309	1402	2432	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.9529	1003	2432	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.6633	1054	2432	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.8452	913	2432	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.5874	703	2432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:51,063] [INFO] DFAST Taxonomy check result was written to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:55:51,064] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:51,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:51,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/checkm_data
[2024-01-24 14:55:51,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:51,131] [INFO] Task started: CheckM
[2024-01-24 14:55:51,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/checkm_input GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:56:53,130] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:53,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:53,162] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:53,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:53,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:56:53,163] [INFO] Task started: Blastn
[2024-01-24 14:56:53,163] [INFO] Running command: blastn -query GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7db97913-ce20-40f0-8b41-96139fb93741/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:55,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:55,221] [INFO] Selected 13 target genomes.
[2024-01-24 14:56:55,221] [INFO] Target genome list was writen to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:55,233] [INFO] Task started: fastANI
[2024-01-24 14:56:55,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgafee2e4a-cce8-4426-9edc-9e6bf02a67cc/GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna.gz --refList GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:18,296] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:18,317] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:18,317] [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_900094585.1	s__Rhizobium multihospitium	100.0	2431	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.86	97.86	0.88	0.88	2	conclusive
GCF_002277895.1	s__Rhizobium sp002277895	91.238	1923	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.72	98.72	0.92	0.92	2	-
GCA_900469175.1	s__Rhizobium sp900469175	91.1786	1883	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	95.56	0.94	0.85	48	-
GCA_900472485.1	s__Rhizobium sp900472485	91.1508	1888	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.96	99.92	0.99	0.98	3	-
GCF_013322215.1	s__Rhizobium rhizogenes_D	91.1285	2041	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900094555.1	s__Rhizobium hainanense	90.4015	2027	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000330885.1	s__Rhizobium tropici	89.1076	1683	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.18	95.15	0.97	0.84	7	-
GCA_900469475.1	s__Rhizobium sp900469475	88.9907	1674	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.70	97.21	0.94	0.88	20	-
GCF_000799755.1	s__Rhizobium tropici_A	88.0277	1857	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.89	99.82	0.97	0.95	4	-
GCA_900468625.1	s__Rhizobium sp900468625	87.6019	1592	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.33	98.37	0.95	0.89	8	-
GCF_000359745.1	s__Rhizobium freirei	86.4145	1550	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207095.1	s__Rhizobium lusitanum_B	85.2476	1549	2432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641435.1	s__Rhizobium sp012641435	85.105	1512	2432	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 14:57:18,319] [INFO] GTDB search result was written to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:18,320] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:18,323] [INFO] DFAST_QC result json was written to GCF_900094585.1_IMG-taxon_2615840698_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:57:18,323] [INFO] DFAST_QC completed!
[2024-01-24 14:57:18,323] [INFO] Total running time: 0h2m11s