[2024-01-25 17:40:50,886] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:50,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:50,888] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference
[2024-01-25 17:40:51,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:51,979] [INFO] Task started: Prodigal
[2024-01-25 17:40:51,980] [INFO] Running command: gunzip -c /var/lib/cwl/stg33229c74-09c9-4200-b598-1678201eecb0/GCF_028598485.1_ASM2859848v1_genomic.fna.gz | prodigal -d GCF_028598485.1_ASM2859848v1_genomic.fna/cds.fna -a GCF_028598485.1_ASM2859848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:04,872] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:04,873] [INFO] Task started: HMMsearch
[2024-01-25 17:41:04,873] [INFO] Running command: hmmsearch --tblout GCF_028598485.1_ASM2859848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/reference_markers.hmm GCF_028598485.1_ASM2859848v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:05,174] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:05,176] [INFO] Found 6/6 markers.
[2024-01-25 17:41:05,222] [INFO] Query marker FASTA was written to GCF_028598485.1_ASM2859848v1_genomic.fna/markers.fasta
[2024-01-25 17:41:05,222] [INFO] Task started: Blastn
[2024-01-25 17:41:05,222] [INFO] Running command: blastn -query GCF_028598485.1_ASM2859848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/reference_markers.fasta -out GCF_028598485.1_ASM2859848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:05,982] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:05,985] [INFO] Selected 21 target genomes.
[2024-01-25 17:41:05,985] [INFO] Target genome list was writen to GCF_028598485.1_ASM2859848v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:06,050] [INFO] Task started: fastANI
[2024-01-25 17:41:06,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg33229c74-09c9-4200-b598-1678201eecb0/GCF_028598485.1_ASM2859848v1_genomic.fna.gz --refList GCF_028598485.1_ASM2859848v1_genomic.fna/target_genomes.txt --output GCF_028598485.1_ASM2859848v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:26,495] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:26,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:26,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:26,505] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:41:26,505] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:41:26,506] [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 miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	93.4271	1185	1519	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	86.3849	989	1519	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	85.8463	1017	1519	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	84.7275	918	1519	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	84.5546	971	1519	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	84.3904	1041	1519	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	84.2483	933	1519	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	84.0896	935	1519	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	83.7839	1023	1519	95	below_threshold
Xenorhabdus nematophila	strain=ATCC 19061	GCA_000252955.1	628	628	type	True	83.3507	929	1519	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.5819	865	1519	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.8689	394	1519	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.7766	420	1519	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	78.7347	401	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:26,507] [INFO] DFAST Taxonomy check result was written to GCF_028598485.1_ASM2859848v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:26,508] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:26,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:26,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/checkm_data
[2024-01-25 17:41:26,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:26,555] [INFO] Task started: CheckM
[2024-01-25 17:41:26,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028598485.1_ASM2859848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028598485.1_ASM2859848v1_genomic.fna/checkm_input GCF_028598485.1_ASM2859848v1_genomic.fna/checkm_result
[2024-01-25 17:42:09,526] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:09,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:09,556] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:09,556] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:09,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028598485.1_ASM2859848v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:09,558] [INFO] Task started: Blastn
[2024-01-25 17:42:09,558] [INFO] Running command: blastn -query GCF_028598485.1_ASM2859848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfeb1fb72-64fb-473f-b3da-389fd077f701/dqc_reference/reference_markers_gtdb.fasta -out GCF_028598485.1_ASM2859848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:10,679] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:10,686] [INFO] Selected 13 target genomes.
[2024-01-25 17:42:10,686] [INFO] Target genome list was writen to GCF_028598485.1_ASM2859848v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:10,715] [INFO] Task started: fastANI
[2024-01-25 17:42:10,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg33229c74-09c9-4200-b598-1678201eecb0/GCF_028598485.1_ASM2859848v1_genomic.fna.gz --refList GCF_028598485.1_ASM2859848v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028598485.1_ASM2859848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:23,831] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:23,839] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:23,840] [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_001037465.1	s__Xenorhabdus khoisanae	97.7721	1239	1519	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_002632615.1	s__Xenorhabdus miraniensis	93.452	1185	1519	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	86.3891	989	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016306625.1	s__Xenorhabdus sp016306625	85.893	1013	1519	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	84.7295	917	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	84.6906	929	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_015163665.1	s__Xenorhabdus sp015163665	84.4066	950	1519	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	84.2073	939	1519	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	84.0864	936	1519	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	83.8113	1022	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.4326	954	1519	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	81.8401	831	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:23,841] [INFO] GTDB search result was written to GCF_028598485.1_ASM2859848v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:23,841] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:23,845] [INFO] DFAST_QC result json was written to GCF_028598485.1_ASM2859848v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:23,845] [INFO] DFAST_QC completed!
[2024-01-25 17:42:23,845] [INFO] Total running time: 0h1m33s