[2024-01-24 12:15:20,396] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference
[2024-01-24 12:15:21,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:21,676] [INFO] Task started: Prodigal
[2024-01-24 12:15:21,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg01351815-8bfa-4089-98ba-1f46ba5a8d9f/GCF_002632685.1_ASM263268v1_genomic.fna.gz | prodigal -d GCF_002632685.1_ASM263268v1_genomic.fna/cds.fna -a GCF_002632685.1_ASM263268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:36,546] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:36,547] [INFO] Task started: HMMsearch
[2024-01-24 12:15:36,547] [INFO] Running command: hmmsearch --tblout GCF_002632685.1_ASM263268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/reference_markers.hmm GCF_002632685.1_ASM263268v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:36,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:36,854] [INFO] Found 6/6 markers.
[2024-01-24 12:15:36,907] [INFO] Query marker FASTA was written to GCF_002632685.1_ASM263268v1_genomic.fna/markers.fasta
[2024-01-24 12:15:36,907] [INFO] Task started: Blastn
[2024-01-24 12:15:36,908] [INFO] Running command: blastn -query GCF_002632685.1_ASM263268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/reference_markers.fasta -out GCF_002632685.1_ASM263268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:37,720] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:37,723] [INFO] Selected 23 target genomes.
[2024-01-24 12:15:37,724] [INFO] Target genome list was writen to GCF_002632685.1_ASM263268v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:37,729] [INFO] Task started: fastANI
[2024-01-24 12:15:37,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg01351815-8bfa-4089-98ba-1f46ba5a8d9f/GCF_002632685.1_ASM263268v1_genomic.fna.gz --refList GCF_002632685.1_ASM263268v1_genomic.fna/target_genomes.txt --output GCF_002632685.1_ASM263268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:59,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:59,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:59,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:59,619] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:59,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:59,620] [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 mauleonii	strain=DSM 17908	GCA_002632685.1	351675	351675	type	True	100.0	1671	1675	95	conclusive
Xenorhabdus mauleonii	strain=DSM 17908	GCA_900113945.1	351675	351675	type	True	99.9759	1640	1675	95	conclusive
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.5613	946	1675	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_002632585.1	290112	290112	type	True	83.3589	962	1675	95	below_threshold
Xenorhabdus koppenhoeferi	strain=DSM 18168	GCA_900116635.1	351659	351659	type	True	83.3097	745	1675	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_000531455.1	290112	290112	type	True	83.288	946	1675	95	below_threshold
Xenorhabdus nematophila	strain=ATCC 19061	GCA_000252955.1	628	628	type	True	83.1925	924	1675	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	82.587	942	1675	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	82.4556	794	1675	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	82.2375	897	1675	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	82.1169	784	1675	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	82.0662	869	1675	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	81.9358	923	1675	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.5563	764	1675	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.7877	353	1675	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.7799	379	1675	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.5081	347	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,622] [INFO] DFAST Taxonomy check result was written to GCF_002632685.1_ASM263268v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:59,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:59,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:59,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/checkm_data
[2024-01-24 12:15:59,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:59,678] [INFO] Task started: CheckM
[2024-01-24 12:15:59,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632685.1_ASM263268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632685.1_ASM263268v1_genomic.fna/checkm_input GCF_002632685.1_ASM263268v1_genomic.fna/checkm_result
[2024-01-24 12:16:47,166] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:47,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:47,191] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:47,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:47,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632685.1_ASM263268v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:47,192] [INFO] Task started: Blastn
[2024-01-24 12:16:47,192] [INFO] Running command: blastn -query GCF_002632685.1_ASM263268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6802539b-92f1-4900-aad7-6f3f09d02969/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632685.1_ASM263268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:48,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:48,167] [INFO] Selected 16 target genomes.
[2024-01-24 12:16:48,167] [INFO] Target genome list was writen to GCF_002632685.1_ASM263268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:48,177] [INFO] Task started: fastANI
[2024-01-24 12:16:48,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg01351815-8bfa-4089-98ba-1f46ba5a8d9f/GCF_002632685.1_ASM263268v1_genomic.fna.gz --refList GCF_002632685.1_ASM263268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632685.1_ASM263268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:05,106] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:05,124] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:05,124] [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_900113945.1	s__Xenorhabdus mauleonii	99.976	1641	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_016306625.1	s__Xenorhabdus sp016306625	83.5533	948	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632585.1	s__Xenorhabdus szentirmaii	83.3519	964	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.85	99.72	0.97	0.94	3	-
GCF_900116635.1	s__Xenorhabdus koppenhoeferi	83.3177	744	1675	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	83.1897	925	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_002632615.1	s__Xenorhabdus miraniensis	82.5719	943	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_001037465.1	s__Xenorhabdus khoisanae	82.5072	942	1675	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	82.4622	794	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	82.2208	898	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632755.1	s__Xenorhabdus ishibashii	82.1032	785	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	82.0558	799	1675	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	81.9587	921	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001908105.1	s__Xenorhabdus eapokensis	81.8714	821	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968175.1	s__Xenorhabdus poinarii	81.7104	704	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.71	96.71	0.87	0.87	2	-
GCF_003386665.1	s__Xenorhabdus cabanillasii	81.6899	730	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_002632485.1	s__Xenorhabdus innexi	81.0809	715	1675	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.93	99.93	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:05,126] [INFO] GTDB search result was written to GCF_002632685.1_ASM263268v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:05,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:05,133] [INFO] DFAST_QC result json was written to GCF_002632685.1_ASM263268v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:05,133] [INFO] DFAST_QC completed!
[2024-01-24 12:17:05,134] [INFO] Total running time: 0h1m45s