[2024-01-24 12:13:28,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference
[2024-01-24 12:13:30,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,120] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,121] [INFO] Running command: gunzip -c /var/lib/cwl/stga38f5a73-981a-4879-8e9f-a7bb5af3bce9/GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/cds.fna -a GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:37,733] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:37,733] [INFO] Task started: HMMsearch
[2024-01-24 12:13:37,734] [INFO] Running command: hmmsearch --tblout GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/reference_markers.hmm GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:38,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:38,075] [INFO] Found 6/6 markers.
[2024-01-24 12:13:38,106] [INFO] Query marker FASTA was written to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:38,107] [INFO] Task started: Blastn
[2024-01-24 12:13:38,107] [INFO] Running command: blastn -query GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/reference_markers.fasta -out GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:38,872] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:38,875] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:38,875] [INFO] Target genome list was writen to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:38,882] [INFO] Task started: fastANI
[2024-01-24 12:13:38,882] [INFO] Running command: fastANI --query /var/lib/cwl/stga38f5a73-981a-4879-8e9f-a7bb5af3bce9/GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna.gz --refList GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:53,580] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:53,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:53,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:53,598] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:53,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:53,598] [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
Xenorhabdus koppenhoeferi	strain=DSM 18168	GCA_900116635.1	351659	351659	type	True	100.0	1004	1008	95	conclusive
Xenorhabdus nematophila	strain=ATCC 19061	GCA_000252955.1	628	628	type	True	87.3866	827	1008	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	85.4719	796	1008	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	83.7734	823	1008	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	83.7646	733	1008	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	83.6801	728	1008	95	below_threshold
Xenorhabdus mauleonii	strain=DSM 17908	GCA_900113945.1	351675	351675	type	True	83.4318	744	1008	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	83.3951	757	1008	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	83.3583	771	1008	95	below_threshold
Xenorhabdus mauleonii	strain=DSM 17908	GCA_002632685.1	351675	351675	type	True	83.3116	748	1008	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	83.1292	752	1008	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.5211	649	1008	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.9382	335	1008	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.9223	323	1008	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.9047	340	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:53,603] [INFO] DFAST Taxonomy check result was written to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:53,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:53,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:53,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/checkm_data
[2024-01-24 12:13:53,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:53,659] [INFO] Task started: CheckM
[2024-01-24 12:13:53,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/checkm_input GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:24,198] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:24,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:24,222] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:24,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:24,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:24,224] [INFO] Task started: Blastn
[2024-01-24 12:14:24,224] [INFO] Running command: blastn -query GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cdc7791-3344-4fb2-bd5e-44c847f08a05/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:25,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:25,251] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:25,251] [INFO] Target genome list was writen to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:25,275] [INFO] Task started: fastANI
[2024-01-24 12:14:25,276] [INFO] Running command: fastANI --query /var/lib/cwl/stga38f5a73-981a-4879-8e9f-a7bb5af3bce9/GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna.gz --refList GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:37,895] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:37,906] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:37,906] [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_900116635.1	s__Xenorhabdus koppenhoeferi	100.0	1004	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000252955.1	s__Xenorhabdus nematophila	87.3613	830	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_016306625.1	s__Xenorhabdus sp016306625	85.4856	795	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001037465.1	s__Xenorhabdus khoisanae	83.9078	770	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632615.1	s__Xenorhabdus miraniensis	83.7711	822	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_900115195.1	s__Xenorhabdus japonica	83.7673	734	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113945.1	s__Xenorhabdus mauleonii	83.3761	748	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003610465.1	s__Xenorhabdus ehlersii	83.3583	771	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_001908105.1	s__Xenorhabdus eapokensis	83.241	718	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632725.1	s__Xenorhabdus hominickii	83.1562	750	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_002632585.1	s__Xenorhabdus szentirmaii	82.632	715	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.85	99.72	0.97	0.94	3	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.5022	708	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:37,908] [INFO] GTDB search result was written to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:37,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:37,912] [INFO] DFAST_QC result json was written to GCF_900116635.1_IMG-taxon_2684622845_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:37,912] [INFO] DFAST_QC completed!
[2024-01-24 12:14:37,912] [INFO] Total running time: 0h1m9s