[2024-01-24 13:26:14,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:14,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:14,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference
[2024-01-24 13:26:15,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:15,718] [INFO] Task started: Prodigal
[2024-01-24 13:26:15,719] [INFO] Running command: gunzip -c /var/lib/cwl/stge6049224-7db2-41e4-b079-8e9863b482f5/GCF_001908105.1_ASM190810v1_genomic.fna.gz | prodigal -d GCF_001908105.1_ASM190810v1_genomic.fna/cds.fna -a GCF_001908105.1_ASM190810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:26,200] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:26,201] [INFO] Task started: HMMsearch
[2024-01-24 13:26:26,201] [INFO] Running command: hmmsearch --tblout GCF_001908105.1_ASM190810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/reference_markers.hmm GCF_001908105.1_ASM190810v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:26,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:26,471] [INFO] Found 6/6 markers.
[2024-01-24 13:26:26,509] [INFO] Query marker FASTA was written to GCF_001908105.1_ASM190810v1_genomic.fna/markers.fasta
[2024-01-24 13:26:26,509] [INFO] Task started: Blastn
[2024-01-24 13:26:26,510] [INFO] Running command: blastn -query GCF_001908105.1_ASM190810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/reference_markers.fasta -out GCF_001908105.1_ASM190810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:27,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:27,326] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:27,327] [INFO] Target genome list was writen to GCF_001908105.1_ASM190810v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:27,350] [INFO] Task started: fastANI
[2024-01-24 13:26:27,350] [INFO] Running command: fastANI --query /var/lib/cwl/stge6049224-7db2-41e4-b079-8e9863b482f5/GCF_001908105.1_ASM190810v1_genomic.fna.gz --refList GCF_001908105.1_ASM190810v1_genomic.fna/target_genomes.txt --output GCF_001908105.1_ASM190810v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:38,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:38,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:38,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:38,720] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:38,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:38,721] [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 eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	100.0	1264	1332	95	conclusive
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	93.2027	966	1332	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	93.0707	1004	1332	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	92.279	1000	1332	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	92.2617	1013	1332	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	87.3774	966	1332	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.6146	894	1332	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	79.0058	373	1332	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.9728	357	1332	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.7973	350	1332	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	78.7835	366	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:38,722] [INFO] DFAST Taxonomy check result was written to GCF_001908105.1_ASM190810v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:38,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:38,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:38,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/checkm_data
[2024-01-24 13:26:38,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:38,773] [INFO] Task started: CheckM
[2024-01-24 13:26:38,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001908105.1_ASM190810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001908105.1_ASM190810v1_genomic.fna/checkm_input GCF_001908105.1_ASM190810v1_genomic.fna/checkm_result
[2024-01-24 13:27:14,162] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:14,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:14,185] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:14,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:14,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001908105.1_ASM190810v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:14,186] [INFO] Task started: Blastn
[2024-01-24 13:27:14,187] [INFO] Running command: blastn -query GCF_001908105.1_ASM190810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb4257b7-21e2-4912-afcc-098b20c7351d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001908105.1_ASM190810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:15,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:15,458] [INFO] Selected 6 target genomes.
[2024-01-24 13:27:15,458] [INFO] Target genome list was writen to GCF_001908105.1_ASM190810v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:15,491] [INFO] Task started: fastANI
[2024-01-24 13:27:15,491] [INFO] Running command: fastANI --query /var/lib/cwl/stge6049224-7db2-41e4-b079-8e9863b482f5/GCF_001908105.1_ASM190810v1_genomic.fna.gz --refList GCF_001908105.1_ASM190810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001908105.1_ASM190810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:22,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:22,480] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:22,481] [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_001908105.1	s__Xenorhabdus eapokensis	100.0	1245	1332	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_001908095.1	s__Xenorhabdus thuongxuanensis	93.1809	968	1332	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	93.0548	1005	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610465.1	s__Xenorhabdus ehlersii	92.2519	1000	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_015163665.1	s__Xenorhabdus sp015163665	90.62	972	1332	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	90.0751	933	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:22,485] [INFO] GTDB search result was written to GCF_001908105.1_ASM190810v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:22,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:22,489] [INFO] DFAST_QC result json was written to GCF_001908105.1_ASM190810v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:22,489] [INFO] DFAST_QC completed!
[2024-01-24 13:27:22,490] [INFO] Total running time: 0h1m8s