[2024-01-24 11:59:35,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference
[2024-01-24 11:59:36,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,627] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,627] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8234b72-0b49-4d03-8478-935809957cb5/GCF_002632445.1_ASM263244v1_genomic.fna.gz | prodigal -d GCF_002632445.1_ASM263244v1_genomic.fna/cds.fna -a GCF_002632445.1_ASM263244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:47,206] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:47,207] [INFO] Task started: HMMsearch
[2024-01-24 11:59:47,207] [INFO] Running command: hmmsearch --tblout GCF_002632445.1_ASM263244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/reference_markers.hmm GCF_002632445.1_ASM263244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:47,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:47,563] [INFO] Found 6/6 markers.
[2024-01-24 11:59:47,602] [INFO] Query marker FASTA was written to GCF_002632445.1_ASM263244v1_genomic.fna/markers.fasta
[2024-01-24 11:59:47,603] [INFO] Task started: Blastn
[2024-01-24 11:59:47,603] [INFO] Running command: blastn -query GCF_002632445.1_ASM263244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/reference_markers.fasta -out GCF_002632445.1_ASM263244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:48,343] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:48,347] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:48,348] [INFO] Target genome list was writen to GCF_002632445.1_ASM263244v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:48,392] [INFO] Task started: fastANI
[2024-01-24 11:59:48,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8234b72-0b49-4d03-8478-935809957cb5/GCF_002632445.1_ASM263244v1_genomic.fna.gz --refList GCF_002632445.1_ASM263244v1_genomic.fna/target_genomes.txt --output GCF_002632445.1_ASM263244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:59,770] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:59,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:59,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:59,786] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:59,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:59,786] [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 ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	100.0	1324	1389	95	conclusive
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	99.9741	1272	1389	95	conclusive
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	93.7074	1015	1389	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	92.2291	1035	1389	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	91.7279	1012	1389	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	87.8549	1016	1389	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	85.008	931	1389	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.3792	772	1389	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.9159	119	1389	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.7855	398	1389	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	77.5827	112	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:59,788] [INFO] DFAST Taxonomy check result was written to GCF_002632445.1_ASM263244v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:59,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:59,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:59,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/checkm_data
[2024-01-24 11:59:59,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:59,832] [INFO] Task started: CheckM
[2024-01-24 11:59:59,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632445.1_ASM263244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632445.1_ASM263244v1_genomic.fna/checkm_input GCF_002632445.1_ASM263244v1_genomic.fna/checkm_result
[2024-01-24 12:00:36,421] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:36,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,449] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:36,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:36,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632445.1_ASM263244v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:36,450] [INFO] Task started: Blastn
[2024-01-24 12:00:36,450] [INFO] Running command: blastn -query GCF_002632445.1_ASM263244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50afcb4c-29ea-43d8-b79f-35b6954777e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632445.1_ASM263244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:37,399] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:37,403] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:37,404] [INFO] Target genome list was writen to GCF_002632445.1_ASM263244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:37,416] [INFO] Task started: fastANI
[2024-01-24 12:00:37,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8234b72-0b49-4d03-8478-935809957cb5/GCF_002632445.1_ASM263244v1_genomic.fna.gz --refList GCF_002632445.1_ASM263244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632445.1_ASM263244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:47,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:47,593] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:47,594] [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_003610465.1	s__Xenorhabdus ehlersii	99.9741	1272	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	conclusive
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	93.6906	1015	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163665.1	s__Xenorhabdus sp015163665	92.8551	1042	1389	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	92.2315	1035	1389	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	91.9074	1005	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632755.1	s__Xenorhabdus ishibashii	91.7293	1012	1389	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	91.6382	987	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_002632615.1	s__Xenorhabdus miraniensis	84.532	973	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	82.1135	781	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:47,595] [INFO] GTDB search result was written to GCF_002632445.1_ASM263244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:47,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:47,599] [INFO] DFAST_QC result json was written to GCF_002632445.1_ASM263244v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:47,599] [INFO] DFAST_QC completed!
[2024-01-24 12:00:47,599] [INFO] Total running time: 0h1m12s