[2024-01-24 14:03:01,875] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:01,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:01,877] [INFO] DQC Reference Directory: /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference
[2024-01-24 14:03:03,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:03,155] [INFO] Task started: Prodigal
[2024-01-24 14:03:03,156] [INFO] Running command: gunzip -c /var/lib/cwl/stgbed3bf6c-08b6-4475-8c5b-a07ab68846c5/GCF_014196295.1_ASM1419629v1_genomic.fna.gz | prodigal -d GCF_014196295.1_ASM1419629v1_genomic.fna/cds.fna -a GCF_014196295.1_ASM1419629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:14,893] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:14,893] [INFO] Task started: HMMsearch
[2024-01-24 14:03:14,893] [INFO] Running command: hmmsearch --tblout GCF_014196295.1_ASM1419629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/reference_markers.hmm GCF_014196295.1_ASM1419629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:15,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:15,205] [INFO] Found 6/6 markers.
[2024-01-24 14:03:15,254] [INFO] Query marker FASTA was written to GCF_014196295.1_ASM1419629v1_genomic.fna/markers.fasta
[2024-01-24 14:03:15,254] [INFO] Task started: Blastn
[2024-01-24 14:03:15,255] [INFO] Running command: blastn -query GCF_014196295.1_ASM1419629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/reference_markers.fasta -out GCF_014196295.1_ASM1419629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:16,251] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:16,256] [INFO] Selected 15 target genomes.
[2024-01-24 14:03:16,257] [INFO] Target genome list was writen to GCF_014196295.1_ASM1419629v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:16,264] [INFO] Task started: fastANI
[2024-01-24 14:03:16,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed3bf6c-08b6-4475-8c5b-a07ab68846c5/GCF_014196295.1_ASM1419629v1_genomic.fna.gz --refList GCF_014196295.1_ASM1419629v1_genomic.fna/target_genomes.txt --output GCF_014196295.1_ASM1419629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:29,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:29,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:29,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:29,646] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:29,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:29,646] [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 haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	100.0	1467	1467	95	conclusive
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	81.2146	815	1467	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.1236	692	1467	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.9563	775	1467	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.4636	713	1467	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.4616	687	1467	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.864	643	1467	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	79.8572	650	1467	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.7657	548	1467	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	79.3847	555	1467	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.3295	642	1467	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	79.2133	463	1467	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.5434	341	1467	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.6881	253	1467	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.5788	192	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:29,648] [INFO] DFAST Taxonomy check result was written to GCF_014196295.1_ASM1419629v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:29,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:29,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:29,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/checkm_data
[2024-01-24 14:03:29,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:29,697] [INFO] Task started: CheckM
[2024-01-24 14:03:29,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196295.1_ASM1419629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196295.1_ASM1419629v1_genomic.fna/checkm_input GCF_014196295.1_ASM1419629v1_genomic.fna/checkm_result
[2024-01-24 14:04:06,459] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:06,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:06,483] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:06,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:06,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196295.1_ASM1419629v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:06,485] [INFO] Task started: Blastn
[2024-01-24 14:04:06,485] [INFO] Running command: blastn -query GCF_014196295.1_ASM1419629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a147e1-3a4c-4cf6-a18f-178cba322abc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196295.1_ASM1419629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:08,518] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:08,522] [INFO] Selected 8 target genomes.
[2024-01-24 14:04:08,522] [INFO] Target genome list was writen to GCF_014196295.1_ASM1419629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:08,531] [INFO] Task started: fastANI
[2024-01-24 14:04:08,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed3bf6c-08b6-4475-8c5b-a07ab68846c5/GCF_014196295.1_ASM1419629v1_genomic.fna.gz --refList GCF_014196295.1_ASM1419629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196295.1_ASM1419629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:16,959] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:16,973] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:16,974] [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_014196295.1	s__Phenylobacterium haematophilum	100.0	1467	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013822795.1	s__Phenylobacterium sp013822795	90.3415	1140	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	90.0923	972	1467	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	89.8323	804	1467	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	88.324	1119	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_001724985.1	s__Phenylobacterium sp001724985	85.3217	625	1467	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	84.1524	979	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	-
GCF_001557235.1	s__Phenylobacterium sp001557235	80.2252	702	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.95	99.95	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:16,976] [INFO] GTDB search result was written to GCF_014196295.1_ASM1419629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:16,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:16,981] [INFO] DFAST_QC result json was written to GCF_014196295.1_ASM1419629v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:16,981] [INFO] DFAST_QC completed!
[2024-01-24 14:04:16,981] [INFO] Total running time: 0h1m15s