[2024-01-24 12:53:37,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference
[2024-01-24 12:53:38,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,503] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,503] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd1cf6e9-c277-464b-9642-9f91985ebcd4/GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/cds.fna -a GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:58,291] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:58,292] [INFO] Task started: HMMsearch
[2024-01-24 12:53:58,292] [INFO] Running command: hmmsearch --tblout GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/reference_markers.hmm GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:58,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:58,608] [INFO] Found 6/6 markers.
[2024-01-24 12:53:58,668] [INFO] Query marker FASTA was written to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:53:58,669] [INFO] Task started: Blastn
[2024-01-24 12:53:58,669] [INFO] Running command: blastn -query GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/reference_markers.fasta -out GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:59,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:59,657] [INFO] Selected 13 target genomes.
[2024-01-24 12:53:59,657] [INFO] Target genome list was writen to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:53:59,664] [INFO] Task started: fastANI
[2024-01-24 12:53:59,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd1cf6e9-c277-464b-9642-9f91985ebcd4/GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna.gz --refList GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:18,091] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:18,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:18,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:18,110] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:18,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:18,111] [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 mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	100.0	2225	2226	95	conclusive
Rhizobium mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	96.0481	1811	2226	95	conclusive
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	96.0092	1842	2226	95	conclusive
Rhizobium gallicum	strain=R602	GCA_000816845.1	56730	56730	type	True	94.045	1826	2226	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.5486	1163	2226	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	81.4723	1104	2226	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	81.3809	1151	2226	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	81.3592	1143	2226	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	81.2896	1132	2226	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	81.2044	1114	2226	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	81.0502	1104	2226	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5129	605	2226	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.0654	634	2226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:18,113] [INFO] DFAST Taxonomy check result was written to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:54:18,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:18,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:18,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/checkm_data
[2024-01-24 12:54:18,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:18,174] [INFO] Task started: CheckM
[2024-01-24 12:54:18,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/checkm_input GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:55:14,019] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:14,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:14,041] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:14,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:14,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:55:14,042] [INFO] Task started: Blastn
[2024-01-24 12:55:14,042] [INFO] Running command: blastn -query GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgad633a93-b3be-4858-b014-6b055cb60b5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:15,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:15,874] [INFO] Selected 6 target genomes.
[2024-01-24 12:55:15,874] [INFO] Target genome list was writen to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:15,883] [INFO] Task started: fastANI
[2024-01-24 12:55:15,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd1cf6e9-c277-464b-9642-9f91985ebcd4/GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna.gz --refList GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:26,825] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:26,838] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:26,838] [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_900099775.1	s__Rhizobium loessense	100.0	2225	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	96.0481	N/A	N/A	N/A	N/A	1	conclusive
GCF_000419765.1	s__Rhizobium mongolense	96.0481	1811	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	96.0481	99.21	97.63	0.93	0.80	4	conclusive
GCF_015353075.1	s__Rhizobium yanglingense	95.1871	1867	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.6157	97.95	97.94	0.79	0.78	3	-
GCF_000816845.1	s__Rhizobium gallicum	94.0327	1828	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.4207	99.69	99.44	0.97	0.94	3	-
GCF_001908375.1	s__Rhizobium etli_B	91.6428	1768	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.26	99.00	0.92	0.87	3	-
GCF_900169785.1	s__Rhizobium sullae	88.7637	1639	2226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.06	97.50	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:26,840] [INFO] GTDB search result was written to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:26,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:26,843] [INFO] DFAST_QC result json was written to GCF_900099775.1_IMG-taxon_2596583570_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:55:26,843] [INFO] DFAST_QC completed!
[2024-01-24 12:55:26,843] [INFO] Total running time: 0h1m50s