[2024-01-25 19:33:20,945] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:20,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:20,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference
[2024-01-25 19:33:22,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,126] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgd18ef54b-fe07-45b2-8225-c6dfad01e177/GCF_022695515.1_ASM2269551v1_genomic.fna.gz | prodigal -d GCF_022695515.1_ASM2269551v1_genomic.fna/cds.fna -a GCF_022695515.1_ASM2269551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:34,125] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:34,126] [INFO] Task started: HMMsearch
[2024-01-25 19:33:34,126] [INFO] Running command: hmmsearch --tblout GCF_022695515.1_ASM2269551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/reference_markers.hmm GCF_022695515.1_ASM2269551v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:34,384] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:34,385] [INFO] Found 6/6 markers.
[2024-01-25 19:33:34,439] [INFO] Query marker FASTA was written to GCF_022695515.1_ASM2269551v1_genomic.fna/markers.fasta
[2024-01-25 19:33:34,439] [INFO] Task started: Blastn
[2024-01-25 19:33:34,439] [INFO] Running command: blastn -query GCF_022695515.1_ASM2269551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/reference_markers.fasta -out GCF_022695515.1_ASM2269551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:35,389] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:35,393] [INFO] Selected 14 target genomes.
[2024-01-25 19:33:35,393] [INFO] Target genome list was writen to GCF_022695515.1_ASM2269551v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:35,397] [INFO] Task started: fastANI
[2024-01-25 19:33:35,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgd18ef54b-fe07-45b2-8225-c6dfad01e177/GCF_022695515.1_ASM2269551v1_genomic.fna.gz --refList GCF_022695515.1_ASM2269551v1_genomic.fna/target_genomes.txt --output GCF_022695515.1_ASM2269551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:49,445] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:49,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:49,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:49,456] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:49,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:49,457] [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
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	100.0	1697	1703	95	conclusive
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	82.5058	898	1703	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.4752	716	1703	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	81.1701	804	1703	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.7666	765	1703	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.4783	727	1703	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.9683	544	1703	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.6109	722	1703	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	79.5721	714	1703	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	79.4651	740	1703	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.3424	735	1703	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	79.3262	732	1703	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.3236	364	1703	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.3036	427	1703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:49,458] [INFO] DFAST Taxonomy check result was written to GCF_022695515.1_ASM2269551v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:49,458] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:49,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:49,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/checkm_data
[2024-01-25 19:33:49,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:49,515] [INFO] Task started: CheckM
[2024-01-25 19:33:49,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022695515.1_ASM2269551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022695515.1_ASM2269551v1_genomic.fna/checkm_input GCF_022695515.1_ASM2269551v1_genomic.fna/checkm_result
[2024-01-25 19:34:26,287] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:26,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:26,308] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:26,308] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:26,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022695515.1_ASM2269551v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:26,310] [INFO] Task started: Blastn
[2024-01-25 19:34:26,310] [INFO] Running command: blastn -query GCF_022695515.1_ASM2269551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fef9cfa-d693-4bdc-95aa-3b4b4635b8ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_022695515.1_ASM2269551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:28,265] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:28,268] [INFO] Selected 21 target genomes.
[2024-01-25 19:34:28,268] [INFO] Target genome list was writen to GCF_022695515.1_ASM2269551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:28,313] [INFO] Task started: fastANI
[2024-01-25 19:34:28,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgd18ef54b-fe07-45b2-8225-c6dfad01e177/GCF_022695515.1_ASM2269551v1_genomic.fna.gz --refList GCF_022695515.1_ASM2269551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022695515.1_ASM2269551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:48,407] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:48,420] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:34:48,421] [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_016772415.1	s__Phenylobacterium sp016772415	82.4782	902	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018001015.1	s__Phenylobacterium sp018001015	82.4614	857	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCA_001724985.1	s__Phenylobacterium sp001724985	82.0551	556	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429025.1	s__Phenylobacterium sp001429025	81.7713	815	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	-
GCA_018240795.1	s__Phenylobacterium sp018240795	81.5056	693	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	81.4807	715	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991675.1	s__Phenylobacterium sp017991675	81.3704	554	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	81.3503	775	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	81.2626	797	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014196295.1	s__Phenylobacterium haematophilum	81.1635	805	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	80.4597	729	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_004799545.1	s__Phenylobacterium sp004799545	80.4438	724	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	80.2866	797	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821435.1	s__Phenylobacterium sp018821435	80.2329	764	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCA_001824475.1	s__Phenylobacterium sp001824475	80.1654	740	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCF_001557235.1	s__Phenylobacterium sp001557235	80.1377	736	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.95	99.95	0.94	0.94	2	-
GCA_016124325.1	s__Phenylobacterium sp016124325	80.0644	720	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003150835.1	s__Phenylobacterium parvum	79.9587	545	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254705.1	s__Phenylobacterium deserti	79.6979	570	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842425.1	s__Phenylobacterium sp903842425	79.6634	397	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243465.1	s__Caulobacter segnis_A	79.4438	620	1703	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:48,422] [INFO] GTDB search result was written to GCF_022695515.1_ASM2269551v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:48,424] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:48,428] [INFO] DFAST_QC result json was written to GCF_022695515.1_ASM2269551v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:48,428] [INFO] DFAST_QC completed!
[2024-01-25 19:34:48,428] [INFO] Total running time: 0h1m27s