[2024-01-24 11:43:34,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:34,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:34,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference
[2024-01-24 11:43:36,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,159] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,160] [INFO] Running command: gunzip -c /var/lib/cwl/stga45a799b-4772-4f7b-88d6-cd55498edb5d/GCF_016772415.1_ASM1677241v2_genomic.fna.gz | prodigal -d GCF_016772415.1_ASM1677241v2_genomic.fna/cds.fna -a GCF_016772415.1_ASM1677241v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:47,970] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:47,971] [INFO] Task started: HMMsearch
[2024-01-24 11:43:47,971] [INFO] Running command: hmmsearch --tblout GCF_016772415.1_ASM1677241v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/reference_markers.hmm GCF_016772415.1_ASM1677241v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:48,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:48,247] [INFO] Found 6/6 markers.
[2024-01-24 11:43:48,290] [INFO] Query marker FASTA was written to GCF_016772415.1_ASM1677241v2_genomic.fna/markers.fasta
[2024-01-24 11:43:48,291] [INFO] Task started: Blastn
[2024-01-24 11:43:48,291] [INFO] Running command: blastn -query GCF_016772415.1_ASM1677241v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/reference_markers.fasta -out GCF_016772415.1_ASM1677241v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:49,263] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:49,267] [INFO] Selected 14 target genomes.
[2024-01-24 11:43:49,268] [INFO] Target genome list was writen to GCF_016772415.1_ASM1677241v2_genomic.fna/target_genomes.txt
[2024-01-24 11:43:49,320] [INFO] Task started: fastANI
[2024-01-24 11:43:49,321] [INFO] Running command: fastANI --query /var/lib/cwl/stga45a799b-4772-4f7b-88d6-cd55498edb5d/GCF_016772415.1_ASM1677241v2_genomic.fna.gz --refList GCF_016772415.1_ASM1677241v2_genomic.fna/target_genomes.txt --output GCF_016772415.1_ASM1677241v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:04,187] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:04,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:04,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:04,203] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:04,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:04,204] [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 glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	100.0	1411	1411	95	conclusive
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	82.443	930	1411	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.4283	736	1411	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	80.9571	766	1411	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.4386	685	1411	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.2575	714	1411	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.7346	636	1411	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	79.4559	652	1411	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	79.391	664	1411	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.3708	644	1411	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	79.3045	650	1411	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	79.2834	621	1411	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.052	339	1411	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.4674	211	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:04,206] [INFO] DFAST Taxonomy check result was written to GCF_016772415.1_ASM1677241v2_genomic.fna/tc_result.tsv
[2024-01-24 11:44:04,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:04,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:04,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/checkm_data
[2024-01-24 11:44:04,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:04,247] [INFO] Task started: CheckM
[2024-01-24 11:44:04,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016772415.1_ASM1677241v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016772415.1_ASM1677241v2_genomic.fna/checkm_input GCF_016772415.1_ASM1677241v2_genomic.fna/checkm_result
[2024-01-24 11:44:40,782] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:40,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:40,808] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:40,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:40,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016772415.1_ASM1677241v2_genomic.fna/markers.fasta)
[2024-01-24 11:44:40,810] [INFO] Task started: Blastn
[2024-01-24 11:44:40,810] [INFO] Running command: blastn -query GCF_016772415.1_ASM1677241v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3932ff9f-43b2-4fec-807f-e219ca5320c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016772415.1_ASM1677241v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:42,835] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:42,839] [INFO] Selected 16 target genomes.
[2024-01-24 11:44:42,839] [INFO] Target genome list was writen to GCF_016772415.1_ASM1677241v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:42,869] [INFO] Task started: fastANI
[2024-01-24 11:44:42,869] [INFO] Running command: fastANI --query /var/lib/cwl/stga45a799b-4772-4f7b-88d6-cd55498edb5d/GCF_016772415.1_ASM1677241v2_genomic.fna.gz --refList GCF_016772415.1_ASM1677241v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016772415.1_ASM1677241v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:00,524] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:00,549] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:00,549] [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	100.0	1411	1411	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_018001015.1	s__Phenylobacterium sp018001015	89.1429	1067	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_001429025.1	s__Phenylobacterium sp001429025	81.94	806	1411	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	81.4294	696	1411	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	81.4184	737	1411	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	81.3751	530	1411	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	81.3362	769	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_013822795.1	s__Phenylobacterium sp013822795	81.1603	778	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799545.1	s__Phenylobacterium sp004799545	80.6457	686	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.5838	706	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254475.1	s__Phenylobacterium soli	80.4507	684	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241625.1	s__Phenylobacterium sp018241625	80.3456	583	1411	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	80.1738	732	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCF_000281955.1	s__Caulobacter sp000281955	79.683	635	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375595.1	s__Phenylobacterium immobile	79.372	436	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909375.1	s__Phenylobacterium sp903909375	79.0217	515	1411	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:00,551] [INFO] GTDB search result was written to GCF_016772415.1_ASM1677241v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:00,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:00,555] [INFO] DFAST_QC result json was written to GCF_016772415.1_ASM1677241v2_genomic.fna/dqc_result.json
[2024-01-24 11:45:00,555] [INFO] DFAST_QC completed!
[2024-01-24 11:45:00,555] [INFO] Total running time: 0h1m26s