[2024-01-24 15:27:22,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:22,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:22,263] [INFO] DQC Reference Directory: /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference
[2024-01-24 15:27:23,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,606] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,606] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4c07345-5699-4b01-aef8-959dd6d7b0c6/GCF_016306625.1_ASM1630662v1_genomic.fna.gz | prodigal -d GCF_016306625.1_ASM1630662v1_genomic.fna/cds.fna -a GCF_016306625.1_ASM1630662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:35,711] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:35,711] [INFO] Task started: HMMsearch
[2024-01-24 15:27:35,711] [INFO] Running command: hmmsearch --tblout GCF_016306625.1_ASM1630662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/reference_markers.hmm GCF_016306625.1_ASM1630662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:36,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:36,041] [INFO] Found 6/6 markers.
[2024-01-24 15:27:36,083] [INFO] Query marker FASTA was written to GCF_016306625.1_ASM1630662v1_genomic.fna/markers.fasta
[2024-01-24 15:27:36,084] [INFO] Task started: Blastn
[2024-01-24 15:27:36,084] [INFO] Running command: blastn -query GCF_016306625.1_ASM1630662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/reference_markers.fasta -out GCF_016306625.1_ASM1630662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:36,861] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:36,866] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:36,866] [INFO] Target genome list was writen to GCF_016306625.1_ASM1630662v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:36,875] [INFO] Task started: fastANI
[2024-01-24 15:27:36,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4c07345-5699-4b01-aef8-959dd6d7b0c6/GCF_016306625.1_ASM1630662v1_genomic.fna.gz --refList GCF_016306625.1_ASM1630662v1_genomic.fna/target_genomes.txt --output GCF_016306625.1_ASM1630662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:55,219] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:55,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:55,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:55,234] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:55,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:55,235] [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 lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	100.0	1378	1381	95	conclusive
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	85.8263	1005	1381	95	below_threshold
Xenorhabdus koppenhoeferi	strain=DSM 18168	GCA_900116635.1	351659	351659	type	True	85.6556	782	1381	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	85.3653	969	1381	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	85.2368	892	1381	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	84.9658	940	1381	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	84.9604	1009	1381	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	84.9452	950	1381	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	84.8379	1011	1381	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	84.7095	904	1381	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	84.6095	895	1381	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	83.2452	905	1381	95	below_threshold
Xenorhabdus innexi	strain=DSM 16336	GCA_002632485.1	290109	290109	type	True	81.4407	724	1381	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.8868	385	1381	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.8746	369	1381	95	below_threshold
Kosakonia cowanii	strain=888-76	GCA_001975225.1	208223	208223	type	True	78.1044	107	1381	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	77.7033	179	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:55,236] [INFO] DFAST Taxonomy check result was written to GCF_016306625.1_ASM1630662v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:55,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:55,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:55,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/checkm_data
[2024-01-24 15:27:55,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:55,283] [INFO] Task started: CheckM
[2024-01-24 15:27:55,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016306625.1_ASM1630662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016306625.1_ASM1630662v1_genomic.fna/checkm_input GCF_016306625.1_ASM1630662v1_genomic.fna/checkm_result
[2024-01-24 15:28:34,187] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:34,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:34,205] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:34,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:34,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016306625.1_ASM1630662v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:34,206] [INFO] Task started: Blastn
[2024-01-24 15:28:34,207] [INFO] Running command: blastn -query GCF_016306625.1_ASM1630662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2ddbc8f-6802-4bc9-a248-fe90bbe1f443/dqc_reference/reference_markers_gtdb.fasta -out GCF_016306625.1_ASM1630662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:35,158] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:35,162] [INFO] Selected 16 target genomes.
[2024-01-24 15:28:35,163] [INFO] Target genome list was writen to GCF_016306625.1_ASM1630662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:35,179] [INFO] Task started: fastANI
[2024-01-24 15:28:35,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4c07345-5699-4b01-aef8-959dd6d7b0c6/GCF_016306625.1_ASM1630662v1_genomic.fna.gz --refList GCF_016306625.1_ASM1630662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016306625.1_ASM1630662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:50,723] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:50,739] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:50,740] [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_016306625.1	s__Xenorhabdus sp016306625	100.0	1378	1381	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_001037465.1	s__Xenorhabdus khoisanae	85.9661	977	1381	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	85.7542	1011	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_002127545.1	s__Xenorhabdus beddingii	85.3633	969	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115195.1	s__Xenorhabdus japonica	85.2699	889	1381	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	84.858	1008	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	84.7208	903	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252955.1	s__Xenorhabdus nematophila	84.6952	933	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_015163665.1	s__Xenorhabdus sp015163665	84.6737	907	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908105.1	s__Xenorhabdus eapokensis	84.608	895	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163655.1	s__Xenorhabdus griffiniae	84.305	916	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	84.2418	888	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	83.1404	907	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.9814	978	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_014467235.1	s__Xenorhabdus indica	81.4979	802	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_900094795.1	s__Kosakonia oryziphila	77.7235	129	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:50,742] [INFO] GTDB search result was written to GCF_016306625.1_ASM1630662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:50,743] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:50,747] [INFO] DFAST_QC result json was written to GCF_016306625.1_ASM1630662v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:50,748] [INFO] DFAST_QC completed!
[2024-01-24 15:28:50,748] [INFO] Total running time: 0h1m28s