[2024-01-24 15:10:41,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,364] [INFO] DQC Reference Directory: /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference
[2024-01-24 15:10:42,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,815] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e3d3ff8-a0da-444d-9b96-4a604dfbe565/GCF_009828105.1_ASM982810v1_genomic.fna.gz | prodigal -d GCF_009828105.1_ASM982810v1_genomic.fna/cds.fna -a GCF_009828105.1_ASM982810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:52,781] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:52,781] [INFO] Task started: HMMsearch
[2024-01-24 15:10:52,781] [INFO] Running command: hmmsearch --tblout GCF_009828105.1_ASM982810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/reference_markers.hmm GCF_009828105.1_ASM982810v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:53,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:53,063] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,096] [INFO] Query marker FASTA was written to GCF_009828105.1_ASM982810v1_genomic.fna/markers.fasta
[2024-01-24 15:10:53,096] [INFO] Task started: Blastn
[2024-01-24 15:10:53,096] [INFO] Running command: blastn -query GCF_009828105.1_ASM982810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/reference_markers.fasta -out GCF_009828105.1_ASM982810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,908] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,917] [INFO] Selected 21 target genomes.
[2024-01-24 15:10:53,917] [INFO] Target genome list was writen to GCF_009828105.1_ASM982810v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:53,928] [INFO] Task started: fastANI
[2024-01-24 15:10:53,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3d3ff8-a0da-444d-9b96-4a604dfbe565/GCF_009828105.1_ASM982810v1_genomic.fna.gz --refList GCF_009828105.1_ASM982810v1_genomic.fna/target_genomes.txt --output GCF_009828105.1_ASM982810v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:06,305] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:06,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:06,321] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:06,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:06,322] [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
Altericroceibacterium indicum	strain=DSM 18604	GCA_009828105.1	374177	374177	type	True	100.0	1026	1026	95	conclusive
Altericroceibacterium spongiae	strain=HN-Y73	GCA_003610805.1	2320269	2320269	type	True	79.4115	456	1026	95	below_threshold
Altericroceibacterium endophyticum	strain=LMG 29518	GCA_009827595.1	1808508	1808508	type	True	78.7178	337	1026	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.1285	243	1026	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.0806	240	1026	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	77.5554	137	1026	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.5034	108	1026	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	77.4564	119	1026	95	below_threshold
Aurantiacibacter atlanticus	strain=s21-N3	GCA_001077815.2	1648404	1648404	type	True	77.4087	131	1026	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	77.3781	141	1026	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.3735	114	1026	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.2463	100	1026	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.1951	121	1026	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.1795	115	1026	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	77.1641	118	1026	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	76.93	205	1026	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	76.8979	141	1026	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	76.696	129	1026	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	76.5202	123	1026	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.4925	91	1026	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	76.4725	94	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,323] [INFO] DFAST Taxonomy check result was written to GCF_009828105.1_ASM982810v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:06,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:06,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:06,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/checkm_data
[2024-01-24 15:11:06,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:06,355] [INFO] Task started: CheckM
[2024-01-24 15:11:06,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828105.1_ASM982810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828105.1_ASM982810v1_genomic.fna/checkm_input GCF_009828105.1_ASM982810v1_genomic.fna/checkm_result
[2024-01-24 15:11:40,982] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:40,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:41,004] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:41,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:41,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828105.1_ASM982810v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:41,006] [INFO] Task started: Blastn
[2024-01-24 15:11:41,006] [INFO] Running command: blastn -query GCF_009828105.1_ASM982810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1660c52a-224b-4429-bbd3-131e71a807d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828105.1_ASM982810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:42,269] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:42,275] [INFO] Selected 22 target genomes.
[2024-01-24 15:11:42,275] [INFO] Target genome list was writen to GCF_009828105.1_ASM982810v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,291] [INFO] Task started: fastANI
[2024-01-24 15:11:42,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3d3ff8-a0da-444d-9b96-4a604dfbe565/GCF_009828105.1_ASM982810v1_genomic.fna.gz --refList GCF_009828105.1_ASM982810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828105.1_ASM982810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:55,929] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:55,953] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:55,953] [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_009828105.1	s__Altericroceibacterium indicum	100.0	1025	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610805.1	s__Altericroceibacterium spongiae	79.4115	456	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827595.1	s__Altericroceibacterium endophyticum	78.7307	336	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.0396	240	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001625325.1	s__Caenibius estronivorus	77.8168	130	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	77.7454	209	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	77.6594	110	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCF_001028705.1	s__Croceicoccus naphthovorans	77.6588	120	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	77.6282	178	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021555.1	s__Alteraurantiacibacter marinus	77.5517	138	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	77.4009	186	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001077815.2	s__Alteraurantiacibacter atlanticus	77.4008	132	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	77.3781	141	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	77.2995	130	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427865.1	s__Croceibacterium sp001427865	77.0178	142	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898545.1	s__Caenibius sp001898545	76.9927	184	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015693305.1	s__Sphingobium sp015693305	76.9781	92	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	76.9305	206	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	76.8344	143	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107685.1	s__Novosphingobium sp008107685	76.6781	105	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196055.1	s__Novosphingobium hassiacum	76.5055	124	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639875.1	s__Blastomonas aquatica	76.4985	92	1026	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:55,955] [INFO] GTDB search result was written to GCF_009828105.1_ASM982810v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:55,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:55,960] [INFO] DFAST_QC result json was written to GCF_009828105.1_ASM982810v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:55,960] [INFO] DFAST_QC completed!
[2024-01-24 15:11:55,960] [INFO] Total running time: 0h1m15s