[2024-01-25 20:27:35,683] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:35,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:35,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference
[2024-01-25 20:27:36,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:36,809] [INFO] Task started: Prodigal
[2024-01-25 20:27:36,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg1abf7031-f60c-4dba-9ab2-adb065aca450/GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/cds.fna -a GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:48,571] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:48,572] [INFO] Task started: HMMsearch
[2024-01-25 20:27:48,572] [INFO] Running command: hmmsearch --tblout GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/reference_markers.hmm GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:48,872] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:48,873] [INFO] Found 6/6 markers.
[2024-01-25 20:27:48,907] [INFO] Query marker FASTA was written to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:27:48,907] [INFO] Task started: Blastn
[2024-01-25 20:27:48,907] [INFO] Running command: blastn -query GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/reference_markers.fasta -out GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:49,886] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:49,888] [INFO] Selected 10 target genomes.
[2024-01-25 20:27:49,889] [INFO] Target genome list was writen to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:27:49,896] [INFO] Task started: fastANI
[2024-01-25 20:27:49,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abf7031-f60c-4dba-9ab2-adb065aca450/GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna.gz --refList GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:59,505] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:59,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:59,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:59,513] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:59,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:59,513] [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
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	100.0	1391	1391	95	conclusive
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	82.7308	1006	1391	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	81.1728	867	1391	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.4709	761	1391	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.7651	676	1391	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.1736	385	1391	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0444	402	1391	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.001	380	1391	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.947	342	1391	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.9368	365	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:59,514] [INFO] DFAST Taxonomy check result was written to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:27:59,516] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:59,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:59,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/checkm_data
[2024-01-25 20:27:59,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:59,560] [INFO] Task started: CheckM
[2024-01-25 20:27:59,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/checkm_input GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:28:37,963] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:37,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:37,983] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:37,983] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:37,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:28:37,984] [INFO] Task started: Blastn
[2024-01-25 20:28:37,984] [INFO] Running command: blastn -query GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgda28e9cd-2494-4493-96d3-b112249fdedd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:39,995] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:39,999] [INFO] Selected 11 target genomes.
[2024-01-25 20:28:39,999] [INFO] Target genome list was writen to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:40,015] [INFO] Task started: fastANI
[2024-01-25 20:28:40,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abf7031-f60c-4dba-9ab2-adb065aca450/GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna.gz --refList GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:51,318] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:51,325] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:51,326] [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_900220985.1	s__Hoeflea halophila	100.0	1391	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002733955.1	s__Hoeflea sp002733955	87.6063	1149	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	82.8293	606	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	82.7405	1004	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_000759435.1	s__Hoeflea sp000759435	81.829	890	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	81.7094	579	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	81.6332	847	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	81.4477	892	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_001011155.1	s__Hoeflea sp001011155	81.2919	858	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	81.1808	866	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	80.4844	758	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:51,327] [INFO] GTDB search result was written to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:51,328] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:51,330] [INFO] DFAST_QC result json was written to GCF_900220985.1_IMG-taxon_2740891889_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:28:51,331] [INFO] DFAST_QC completed!
[2024-01-25 20:28:51,331] [INFO] Total running time: 0h1m16s