[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,935] [INFO] DQC Reference Directory: /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,819] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c2033ce-66a1-4e80-9c84-2e8277d0602f/GCF_009827295.1_ASM982729v1_genomic.fna.gz | prodigal -d GCF_009827295.1_ASM982729v1_genomic.fna/cds.fna -a GCF_009827295.1_ASM982729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:13,582] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:13,583] [INFO] Task started: HMMsearch
[2024-01-24 11:05:13,583] [INFO] Running command: hmmsearch --tblout GCF_009827295.1_ASM982729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/reference_markers.hmm GCF_009827295.1_ASM982729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:13,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:13,869] [INFO] Found 6/6 markers.
[2024-01-24 11:05:13,895] [INFO] Query marker FASTA was written to GCF_009827295.1_ASM982729v1_genomic.fna/markers.fasta
[2024-01-24 11:05:13,895] [INFO] Task started: Blastn
[2024-01-24 11:05:13,896] [INFO] Running command: blastn -query GCF_009827295.1_ASM982729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/reference_markers.fasta -out GCF_009827295.1_ASM982729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:14,763] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:14,766] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:14,766] [INFO] Target genome list was writen to GCF_009827295.1_ASM982729v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:14,772] [INFO] Task started: fastANI
[2024-01-24 11:05:14,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c2033ce-66a1-4e80-9c84-2e8277d0602f/GCF_009827295.1_ASM982729v1_genomic.fna.gz --refList GCF_009827295.1_ASM982729v1_genomic.fna/target_genomes.txt --output GCF_009827295.1_ASM982729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:28,065] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:28,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:28,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:28,078] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:28,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:28,078] [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 pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	100.0	1005	1006	95	conclusive
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.4729	533	1006	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	80.2561	497	1006	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.1221	552	1006	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	80.0956	487	1006	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	80.0817	514	1006	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.0534	521	1006	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.0181	507	1006	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	79.9805	442	1006	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.9287	488	1006	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.8254	456	1006	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.7805	443	1006	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.6278	462	1006	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	79.5238	460	1006	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5058	459	1006	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	79.4041	436	1006	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	79.3968	473	1006	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	79.3621	417	1006	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.342	434	1006	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	78.9602	416	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:28,079] [INFO] DFAST Taxonomy check result was written to GCF_009827295.1_ASM982729v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:28,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:28,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:28,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/checkm_data
[2024-01-24 11:05:28,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:28,111] [INFO] Task started: CheckM
[2024-01-24 11:05:28,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827295.1_ASM982729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827295.1_ASM982729v1_genomic.fna/checkm_input GCF_009827295.1_ASM982729v1_genomic.fna/checkm_result
[2024-01-24 11:05:54,272] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:54,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:54,290] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:54,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:54,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827295.1_ASM982729v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:54,291] [INFO] Task started: Blastn
[2024-01-24 11:05:54,291] [INFO] Running command: blastn -query GCF_009827295.1_ASM982729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77f2ade-e985-4b39-bcf6-ce7c118e6e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827295.1_ASM982729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,006] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:56,006] [INFO] Target genome list was writen to GCF_009827295.1_ASM982729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:56,014] [INFO] Task started: fastANI
[2024-01-24 11:05:56,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c2033ce-66a1-4e80-9c84-2e8277d0602f/GCF_009827295.1_ASM982729v1_genomic.fna.gz --refList GCF_009827295.1_ASM982729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827295.1_ASM982729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:04,546] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:04,554] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:04,555] [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_009827295.1	s__Qipengyuania pelagi	100.0	1005	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009993605.1	s__Qipengyuania sp009993605	91.3321	803	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	87.5139	739	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_009828015.1	s__Qipengyuania citrea	81.1656	551	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCF_015767595.1	s__Qipengyuania sp002895025	80.6606	457	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCA_018828205.1	s__Qipengyuania sp018828205	80.6296	475	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	80.4896	411	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	80.328	554	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	80.0716	515	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.0643	520	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	80.0322	451	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	79.9816	372	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCF_015529805.1	s__Qipengyuania soli	79.5058	459	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:04,556] [INFO] GTDB search result was written to GCF_009827295.1_ASM982729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:04,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:04,560] [INFO] DFAST_QC result json was written to GCF_009827295.1_ASM982729v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:04,560] [INFO] DFAST_QC completed!
[2024-01-24 11:06:04,560] [INFO] Total running time: 0h1m1s