[2024-01-24 12:53:53,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:53,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:53,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference
[2024-01-24 12:53:55,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:55,095] [INFO] Task started: Prodigal
[2024-01-24 12:53:55,095] [INFO] Running command: gunzip -c /var/lib/cwl/stge045eb27-97cb-4432-9aa4-7514060260c2/GCF_004352825.1_ASM435282v1_genomic.fna.gz | prodigal -d GCF_004352825.1_ASM435282v1_genomic.fna/cds.fna -a GCF_004352825.1_ASM435282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:03,844] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:03,844] [INFO] Task started: HMMsearch
[2024-01-24 12:54:03,844] [INFO] Running command: hmmsearch --tblout GCF_004352825.1_ASM435282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/reference_markers.hmm GCF_004352825.1_ASM435282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:04,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:04,117] [INFO] Found 6/6 markers.
[2024-01-24 12:54:04,148] [INFO] Query marker FASTA was written to GCF_004352825.1_ASM435282v1_genomic.fna/markers.fasta
[2024-01-24 12:54:04,149] [INFO] Task started: Blastn
[2024-01-24 12:54:04,149] [INFO] Running command: blastn -query GCF_004352825.1_ASM435282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/reference_markers.fasta -out GCF_004352825.1_ASM435282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:05,238] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:05,242] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:05,242] [INFO] Target genome list was writen to GCF_004352825.1_ASM435282v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:05,284] [INFO] Task started: fastANI
[2024-01-24 12:54:05,284] [INFO] Running command: fastANI --query /var/lib/cwl/stge045eb27-97cb-4432-9aa4-7514060260c2/GCF_004352825.1_ASM435282v1_genomic.fna.gz --refList GCF_004352825.1_ASM435282v1_genomic.fna/target_genomes.txt --output GCF_004352825.1_ASM435282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:14,924] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:14,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:14,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:14,936] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:14,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:14,937] [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
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	100.0	985	985	95	conclusive
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	89.4491	797	985	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	88.7521	807	985	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	88.03	751	985	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	87.9998	768	985	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	86.9078	725	985	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.879	642	985	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	82.623	681	985	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	82.3636	657	985	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	81.6943	503	985	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	81.6465	512	985	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.1557	608	985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:14,938] [INFO] DFAST Taxonomy check result was written to GCF_004352825.1_ASM435282v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:14,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:14,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:14,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/checkm_data
[2024-01-24 12:54:14,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:14,974] [INFO] Task started: CheckM
[2024-01-24 12:54:14,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004352825.1_ASM435282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004352825.1_ASM435282v1_genomic.fna/checkm_input GCF_004352825.1_ASM435282v1_genomic.fna/checkm_result
[2024-01-24 12:55:01,254] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:01,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:01,278] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:01,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:01,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004352825.1_ASM435282v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:01,279] [INFO] Task started: Blastn
[2024-01-24 12:55:01,279] [INFO] Running command: blastn -query GCF_004352825.1_ASM435282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dddd45c-7107-42ab-a9f4-72a44dc2d49b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004352825.1_ASM435282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:03,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:03,331] [INFO] Selected 8 target genomes.
[2024-01-24 12:55:03,331] [INFO] Target genome list was writen to GCF_004352825.1_ASM435282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:03,336] [INFO] Task started: fastANI
[2024-01-24 12:55:03,337] [INFO] Running command: fastANI --query /var/lib/cwl/stge045eb27-97cb-4432-9aa4-7514060260c2/GCF_004352825.1_ASM435282v1_genomic.fna.gz --refList GCF_004352825.1_ASM435282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004352825.1_ASM435282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:09,334] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:09,341] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:09,342] [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_004352825.1	s__Luteimonas arsenica	100.0	985	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652935.1	s__Luteimonas padinae	89.4465	797	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	88.7345	808	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	88.0296	751	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016615955.1	s__Luteimonas sp016615955	87.5094	777	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_007795095.1	s__Luteimonas granuli	86.9078	725	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012510865.1	s__Luteimonas sp012510865	86.1116	499	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	81.5694	518	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:09,343] [INFO] GTDB search result was written to GCF_004352825.1_ASM435282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:09,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:09,347] [INFO] DFAST_QC result json was written to GCF_004352825.1_ASM435282v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:09,347] [INFO] DFAST_QC completed!
[2024-01-24 12:55:09,347] [INFO] Total running time: 0h1m15s