[2024-01-24 12:13:06,158] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:06,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:06,172] [INFO] DQC Reference Directory: /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference
[2024-01-24 12:13:07,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,398] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f1becd8-3692-4176-b5b4-0ab41a38f28e/GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/cds.fna -a GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:21,956] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:21,957] [INFO] Task started: HMMsearch
[2024-01-24 12:13:21,957] [INFO] Running command: hmmsearch --tblout GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/reference_markers.hmm GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:22,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:22,197] [INFO] Found 6/6 markers.
[2024-01-24 12:13:22,236] [INFO] Query marker FASTA was written to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:22,237] [INFO] Task started: Blastn
[2024-01-24 12:13:22,237] [INFO] Running command: blastn -query GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/reference_markers.fasta -out GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:22,985] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:22,990] [INFO] Selected 23 target genomes.
[2024-01-24 12:13:22,991] [INFO] Target genome list was writen to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:23,034] [INFO] Task started: fastANI
[2024-01-24 12:13:23,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f1becd8-3692-4176-b5b4-0ab41a38f28e/GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna.gz --refList GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:44,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:44,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:44,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:44,157] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:44,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:44,158] [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_900113945.1	351675	351675	type	True	100.0	1647	1655	95	conclusive
Xenorhabdus mauleonii	strain=DSM 17908	GCA_002632685.1	351675	351675	type	True	99.9881	1647	1655	95	conclusive
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.4205	959	1655	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_002632585.1	290112	290112	type	True	83.3924	968	1655	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_000531455.1	290112	290112	type	True	83.2931	929	1655	95	below_threshold
Xenorhabdus koppenhoeferi	strain=DSM 18168	GCA_900116635.1	351659	351659	type	True	83.1819	744	1655	95	below_threshold
Xenorhabdus nematophila	strain=ATCC 19061	GCA_000252955.1	628	628	type	True	83.1682	925	1655	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	82.5233	942	1655	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	82.5179	799	1655	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	82.2063	900	1655	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	82.1959	833	1655	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	82.0939	793	1655	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	81.9451	910	1655	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.4551	772	1655	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.7567	375	1655	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.6227	357	1655	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.4859	344	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:44,159] [INFO] DFAST Taxonomy check result was written to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:44,160] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:44,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:44,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/checkm_data
[2024-01-24 12:13:44,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:44,209] [INFO] Task started: CheckM
[2024-01-24 12:13:44,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/checkm_input GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:30,948] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:30,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:30,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:30,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:30,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:30,974] [INFO] Task started: Blastn
[2024-01-24 12:14:30,974] [INFO] Running command: blastn -query GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga4497dd7-363c-41c3-92ad-e0b519331104/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:31,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:31,920] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:31,920] [INFO] Target genome list was writen to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:31,930] [INFO] Task started: fastANI
[2024-01-24 12:14:31,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f1becd8-3692-4176-b5b4-0ab41a38f28e/GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna.gz --refList GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:48,148] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:48,165] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:48,165] [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	100.0	1647	1655	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	83.4014	961	1655	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	83.3792	968	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.85	99.72	0.97	0.94	3	-
GCF_000252955.1	s__Xenorhabdus nematophila	83.1884	924	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_900116635.1	s__Xenorhabdus koppenhoeferi	83.1544	747	1655	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	82.5916	932	1655	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	82.5315	940	1655	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	82.5223	799	1655	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	82.226	897	1655	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	82.0781	796	1655	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	81.9841	828	1655	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	81.9676	802	1655	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	81.9627	906	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000968175.1	s__Xenorhabdus poinarii	81.6776	690	1655	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	81.6114	724	1655	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	80.9039	717	1655	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 12:14:48,176] [INFO] GTDB search result was written to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:48,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:48,184] [INFO] DFAST_QC result json was written to GCF_900113945.1_IMG-taxon_2684622849_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:48,184] [INFO] DFAST_QC completed!
[2024-01-24 12:14:48,184] [INFO] Total running time: 0h1m42s