[2024-01-25 19:44:20,907] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:20,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:20,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference
[2024-01-25 19:44:22,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:22,062] [INFO] Task started: Prodigal
[2024-01-25 19:44:22,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb8f300d-9794-466f-9ca4-5b8d69e644ba/GCF_009827655.1_ASM982765v1_genomic.fna.gz | prodigal -d GCF_009827655.1_ASM982765v1_genomic.fna/cds.fna -a GCF_009827655.1_ASM982765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:32,749] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:32,750] [INFO] Task started: HMMsearch
[2024-01-25 19:44:32,750] [INFO] Running command: hmmsearch --tblout GCF_009827655.1_ASM982765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/reference_markers.hmm GCF_009827655.1_ASM982765v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:32,967] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:32,968] [INFO] Found 6/6 markers.
[2024-01-25 19:44:33,000] [INFO] Query marker FASTA was written to GCF_009827655.1_ASM982765v1_genomic.fna/markers.fasta
[2024-01-25 19:44:33,001] [INFO] Task started: Blastn
[2024-01-25 19:44:33,001] [INFO] Running command: blastn -query GCF_009827655.1_ASM982765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/reference_markers.fasta -out GCF_009827655.1_ASM982765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:33,888] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:33,890] [INFO] Selected 27 target genomes.
[2024-01-25 19:44:33,891] [INFO] Target genome list was writen to GCF_009827655.1_ASM982765v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:33,906] [INFO] Task started: fastANI
[2024-01-25 19:44:33,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8f300d-9794-466f-9ca4-5b8d69e644ba/GCF_009827655.1_ASM982765v1_genomic.fna.gz --refList GCF_009827655.1_ASM982765v1_genomic.fna/target_genomes.txt --output GCF_009827655.1_ASM982765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:51,391] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:51,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:51,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:51,407] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:44:51,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:44:51,407] [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
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	80.0246	424	1247	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.891	568	1247	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.5289	458	1247	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	79.2917	404	1247	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	79.2743	440	1247	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	79.0103	412	1247	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	78.9509	332	1247	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.9395	414	1247	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.9168	420	1247	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.9017	413	1247	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.8948	475	1247	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	78.8845	350	1247	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.8445	351	1247	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.808	363	1247	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.7772	400	1247	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.764	369	1247	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.747	432	1247	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.7342	336	1247	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.7182	328	1247	95	below_threshold
Novosphingobium ginsenosidimutans	strain=FW-6	GCA_007954425.1	1176536	1176536	type	True	78.7064	350	1247	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.6981	355	1247	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	78.5988	400	1247	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	78.5343	408	1247	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.4324	367	1247	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	78.4068	316	1247	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.1164	298	1247	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0763	240	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:51,409] [INFO] DFAST Taxonomy check result was written to GCF_009827655.1_ASM982765v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:51,409] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:51,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:51,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/checkm_data
[2024-01-25 19:44:51,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:51,450] [INFO] Task started: CheckM
[2024-01-25 19:44:51,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827655.1_ASM982765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827655.1_ASM982765v1_genomic.fna/checkm_input GCF_009827655.1_ASM982765v1_genomic.fna/checkm_result
[2024-01-25 19:45:24,936] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:24,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:24,952] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:24,952] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:24,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827655.1_ASM982765v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:24,953] [INFO] Task started: Blastn
[2024-01-25 19:45:24,953] [INFO] Running command: blastn -query GCF_009827655.1_ASM982765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e1a491-1d91-4838-ab95-4aa92a45ef83/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827655.1_ASM982765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:26,723] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:26,726] [INFO] Selected 26 target genomes.
[2024-01-25 19:45:26,726] [INFO] Target genome list was writen to GCF_009827655.1_ASM982765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:26,749] [INFO] Task started: fastANI
[2024-01-25 19:45:26,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8f300d-9794-466f-9ca4-5b8d69e644ba/GCF_009827655.1_ASM982765v1_genomic.fna.gz --refList GCF_009827655.1_ASM982765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827655.1_ASM982765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:43,764] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:43,779] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:43,780] [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_009827655.1	s__Alteraurantiacibacter buctensis	100.0	1247	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	80.2953	625	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	80.0173	425	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	79.7709	522	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584125.1	s__Alteraurantiacibacter zhengii	79.5669	455	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	79.5294	530	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	79.3472	403	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	79.3225	479	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660445.1	s__Croceibacterium ferulae	79.2927	405	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	79.229	397	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337385.1	s__Alteraurantiacibacter sp002337385	79.2282	451	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.1113	428	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000802385.1	s__Croceibacterium mercuriale	79.0105	412	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.9015	413	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.8948	475	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677335.1	s__Erythrobacter dokdonensis	78.8445	351	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.8084	363	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.7701	364	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	78.7471	335	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954425.1	s__Novosphingobium ginsenosidimutans	78.7064	350	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.691	355	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657645.1	s__Novosphingobium sp015657645	78.686	347	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440635.1	s__Novosphingobium sp002440635	78.6062	368	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341345.1	s__Alteraurantiacibacter sp002341345	78.6056	298	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	78.5286	408	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822005.1	s__Novosphingobium sp013822005	78.2743	294	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:43,781] [INFO] GTDB search result was written to GCF_009827655.1_ASM982765v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:43,782] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:43,786] [INFO] DFAST_QC result json was written to GCF_009827655.1_ASM982765v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:43,786] [INFO] DFAST_QC completed!
[2024-01-25 19:45:43,786] [INFO] Total running time: 0h1m23s