[2024-01-24 12:15:20,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference
[2024-01-24 12:15:22,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,095] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,095] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3268ede-08b9-4d1b-b8f0-afca0743cf47/GCF_009827635.1_ASM982763v1_genomic.fna.gz | prodigal -d GCF_009827635.1_ASM982763v1_genomic.fna/cds.fna -a GCF_009827635.1_ASM982763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,536] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,537] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,537] [INFO] Running command: hmmsearch --tblout GCF_009827635.1_ASM982763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/reference_markers.hmm GCF_009827635.1_ASM982763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:30,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:30,801] [INFO] Found 6/6 markers.
[2024-01-24 12:15:30,831] [INFO] Query marker FASTA was written to GCF_009827635.1_ASM982763v1_genomic.fna/markers.fasta
[2024-01-24 12:15:30,832] [INFO] Task started: Blastn
[2024-01-24 12:15:30,832] [INFO] Running command: blastn -query GCF_009827635.1_ASM982763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/reference_markers.fasta -out GCF_009827635.1_ASM982763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,589] [INFO] Selected 30 target genomes.
[2024-01-24 12:15:31,590] [INFO] Target genome list was writen to GCF_009827635.1_ASM982763v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:31,602] [INFO] Task started: fastANI
[2024-01-24 12:15:31,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3268ede-08b9-4d1b-b8f0-afca0743cf47/GCF_009827635.1_ASM982763v1_genomic.fna.gz --refList GCF_009827635.1_ASM982763v1_genomic.fna/target_genomes.txt --output GCF_009827635.1_ASM982763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:48,211] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:48,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:48,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:48,235] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:48,235] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:48,235] [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
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.2216	336	962	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	78.673	340	962	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6554	341	962	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.6204	349	962	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	78.6012	305	962	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	78.5892	257	962	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.5101	340	962	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.4333	370	962	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.4262	333	962	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.3884	273	962	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	78.3452	326	962	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	78.3244	319	962	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	78.31	294	962	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.2741	288	962	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	78.2669	269	962	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.2163	329	962	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	78.1126	245	962	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	78.0805	239	962	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	78.0503	226	962	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.0389	278	962	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.0061	324	962	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	77.9924	244	962	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	77.9734	273	962	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.837	295	962	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.5356	269	962	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.5165	205	962	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.4443	219	962	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	77.0991	143	962	95	below_threshold
Novosphingobium guangzhouense	strain=SA925	GCA_002896965.1	1850347	1850347	type	True	77.0482	185	962	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	76.9528	160	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:48,237] [INFO] DFAST Taxonomy check result was written to GCF_009827635.1_ASM982763v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:48,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:48,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:48,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/checkm_data
[2024-01-24 12:15:48,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:48,273] [INFO] Task started: CheckM
[2024-01-24 12:15:48,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827635.1_ASM982763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827635.1_ASM982763v1_genomic.fna/checkm_input GCF_009827635.1_ASM982763v1_genomic.fna/checkm_result
[2024-01-24 12:16:16,627] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:16,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,651] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:16,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:16,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827635.1_ASM982763v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:16,652] [INFO] Task started: Blastn
[2024-01-24 12:16:16,652] [INFO] Running command: blastn -query GCF_009827635.1_ASM982763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bee8cf0-51f1-4fa2-bd5c-52d6f10b11f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827635.1_ASM982763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:17,744] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:17,749] [INFO] Selected 25 target genomes.
[2024-01-24 12:16:17,749] [INFO] Target genome list was writen to GCF_009827635.1_ASM982763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:17,772] [INFO] Task started: fastANI
[2024-01-24 12:16:17,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3268ede-08b9-4d1b-b8f0-afca0743cf47/GCF_009827635.1_ASM982763v1_genomic.fna.gz --refList GCF_009827635.1_ASM982763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827635.1_ASM982763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:32,488] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:32,520] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:32,521] [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_009827635.1	s__Parapontixanthobacter aurantiacus	100.0	961	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parapontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013370205.1	s__Actirhodobacter atriluteus	80.1106	443	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	80.0138	343	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	79.0112	290	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	78.803	357	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.7238	379	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.5962	319	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	78.4775	308	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.4633	347	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661675.2	s__Croceicoccus marinus	78.2213	268	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.1952	324	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155425.1	s__Erythrobacter donghaensis	78.0406	279	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.9791	286	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009827435.1	s__Croceibacterium salegens	77.9603	239	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	77.9484	242	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002278985.1	s__34-65-8 sp002278985	77.9382	159	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__34-65-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013336795.1	s__Pseudopontixanthobacter muriae	77.8702	269	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	77.8584	237	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003724185.1	s__Erythrobacter sp003724185	77.7796	261	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557115.1	s__Erythrobacter sp001557115	77.6493	276	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCA_017744735.1	s__Caenibius sp017744735	77.5605	238	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	77.5448	270	962	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_001298105.1	s__Novosphingobium sp001298105	77.3569	193	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.11	98.61	0.92	0.87	4	-
GCA_013791705.1	s__Novosphingobium sp013791705	77.1061	162	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
GCF_002896965.1	s__Novosphingobium guangzhouense	77.0482	185	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:32,522] [INFO] GTDB search result was written to GCF_009827635.1_ASM982763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:32,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:32,531] [INFO] DFAST_QC result json was written to GCF_009827635.1_ASM982763v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:32,531] [INFO] DFAST_QC completed!
[2024-01-24 12:16:32,531] [INFO] Total running time: 0h1m12s