[2024-01-24 12:46:57,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference
[2024-01-24 12:46:58,568] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:58,570] [INFO] Task started: Prodigal
[2024-01-24 12:46:58,571] [INFO] Running command: gunzip -c /var/lib/cwl/stgabd8b5ca-5e4c-430c-b161-ccf394f4264e/GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/cds.fna -a GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:19,310] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:19,310] [INFO] Task started: HMMsearch
[2024-01-24 12:47:19,311] [INFO] Running command: hmmsearch --tblout GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/reference_markers.hmm GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:19,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:19,655] [INFO] Found 6/6 markers.
[2024-01-24 12:47:19,715] [INFO] Query marker FASTA was written to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:19,716] [INFO] Task started: Blastn
[2024-01-24 12:47:19,716] [INFO] Running command: blastn -query GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/reference_markers.fasta -out GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:20,717] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:20,720] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:20,720] [INFO] Target genome list was writen to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:20,727] [INFO] Task started: fastANI
[2024-01-24 12:47:20,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd8b5ca-5e4c-430c-b161-ccf394f4264e/GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna.gz --refList GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:39,418] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:39,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:39,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:39,430] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:47:39,430] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:47:39,431] [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 tibeticum	strain=CGMCC 1.7071	GCA_900110205.1	501024	501024	type	True	100.0	2258	2267	95	inconclusive
Rhizobium tibeticum		GCA_900108425.1	501024	501024	type	True	99.9773	2184	2267	95	inconclusive
Rhizobium favelukesii	strain=LPU83	GCA_000577275.2	348824	348824	type	True	95.4501	1875	2267	95	inconclusive
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	86.2611	1468	2267	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	85.5824	1401	2267	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.1818	1038	2267	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	81.1346	1093	2267	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.0345	1037	2267	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	80.9694	1041	2267	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.8805	1060	2267	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.3261	592	2267	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.9625	612	2267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:39,432] [INFO] DFAST Taxonomy check result was written to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:39,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:39,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:39,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/checkm_data
[2024-01-24 12:47:39,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:39,501] [INFO] Task started: CheckM
[2024-01-24 12:47:39,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/checkm_input GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:48:38,304] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:38,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:38,326] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:38,327] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:38,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:48:38,328] [INFO] Task started: Blastn
[2024-01-24 12:48:38,328] [INFO] Running command: blastn -query GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6b6ec1-7bf0-4e39-81dc-e55506137de8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:40,221] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:40,225] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:40,225] [INFO] Target genome list was writen to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:40,234] [INFO] Task started: fastANI
[2024-01-24 12:48:40,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd8b5ca-5e4c-430c-b161-ccf394f4264e/GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna.gz --refList GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:57,850] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:57,866] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:57,866] [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_900110205.1	s__Rhizobium tibeticum	100.0	2259	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.5244	99.98	99.98	0.99	0.99	2	conclusive
GCF_000577275.2	s__Rhizobium favelukesii	95.4546	1874	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.5244	99.59	99.23	0.94	0.89	3	-
GCF_000799845.1	s__Rhizobium sp000799845	95.2651	1760	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.2724	99.41	99.41	0.91	0.91	2	-
GCF_000282035.1	s__Rhizobium sp000282035	88.9766	1525	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.50	0.88	0.87	4	-
GCF_002211365.1	s__Rhizobium sp002211365	86.6248	1414	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.54	97.07	0.93	0.86	3	-
GCF_001542405.1	s__Rhizobium altiplani	86.2491	1470	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.38	95.34	0.86	0.71	19	-
GCA_900466605.1	s__Rhizobium sp900466605	85.9586	1348	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194695.1	s__Rhizobium sp014194695	85.6552	1339	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.49	98.48	0.95	0.94	4	-
GCF_000298315.2	s__Rhizobium grahamii	85.5808	1401	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.32	97.32	0.91	0.91	2	-
GCF_000746265.1	s__Rhizobium sp000746265	85.1026	1340	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746385.1	s__Rhizobium sp000746385	82.1997	1035	2267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.83	96.83	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,867] [INFO] GTDB search result was written to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:57,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:57,872] [INFO] DFAST_QC result json was written to GCF_900110205.1_IMG-taxon_2671180023_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:57,872] [INFO] DFAST_QC completed!
[2024-01-24 12:48:57,872] [INFO] Total running time: 0h2m1s