[2024-01-25 20:26:35,840] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference
[2024-01-25 20:26:37,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,022] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,022] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfe145ae-3ada-4069-81df-09ccec1c423e/GCF_009827535.1_ASM982753v1_genomic.fna.gz | prodigal -d GCF_009827535.1_ASM982753v1_genomic.fna/cds.fna -a GCF_009827535.1_ASM982753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:44,543] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:44,544] [INFO] Task started: HMMsearch
[2024-01-25 20:26:44,544] [INFO] Running command: hmmsearch --tblout GCF_009827535.1_ASM982753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/reference_markers.hmm GCF_009827535.1_ASM982753v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:44,733] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:44,734] [INFO] Found 6/6 markers.
[2024-01-25 20:26:44,759] [INFO] Query marker FASTA was written to GCF_009827535.1_ASM982753v1_genomic.fna/markers.fasta
[2024-01-25 20:26:44,759] [INFO] Task started: Blastn
[2024-01-25 20:26:44,759] [INFO] Running command: blastn -query GCF_009827535.1_ASM982753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/reference_markers.fasta -out GCF_009827535.1_ASM982753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:45,624] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:45,626] [INFO] Selected 20 target genomes.
[2024-01-25 20:26:45,626] [INFO] Target genome list was writen to GCF_009827535.1_ASM982753v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:45,686] [INFO] Task started: fastANI
[2024-01-25 20:26:45,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe145ae-3ada-4069-81df-09ccec1c423e/GCF_009827535.1_ASM982753v1_genomic.fna.gz --refList GCF_009827535.1_ASM982753v1_genomic.fna/target_genomes.txt --output GCF_009827535.1_ASM982753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:56,979] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:56,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:56,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:56,991] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:26:56,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:26:56,992] [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 proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.5553	506	951	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.4969	467	951	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	80.1161	466	951	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	80.0906	448	951	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	80.0387	482	951	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	80.0152	451	951	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	79.9965	472	951	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	79.9667	459	951	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.9309	440	951	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.804	437	951	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.7607	450	951	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.5853	398	951	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.5799	424	951	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.5354	436	951	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	79.5284	476	951	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	79.4857	459	951	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	79.4301	422	951	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	79.144	398	951	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	79.0842	401	951	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	78.7361	323	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:57,006] [INFO] DFAST Taxonomy check result was written to GCF_009827535.1_ASM982753v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:57,007] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:57,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:57,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/checkm_data
[2024-01-25 20:26:57,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:57,036] [INFO] Task started: CheckM
[2024-01-25 20:26:57,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827535.1_ASM982753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827535.1_ASM982753v1_genomic.fna/checkm_input GCF_009827535.1_ASM982753v1_genomic.fna/checkm_result
[2024-01-25 20:27:22,715] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:22,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:22,742] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:22,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:22,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827535.1_ASM982753v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:22,743] [INFO] Task started: Blastn
[2024-01-25 20:27:22,743] [INFO] Running command: blastn -query GCF_009827535.1_ASM982753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119a2e76-20e3-4efc-b00a-77856289c0e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827535.1_ASM982753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:24,483] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:24,486] [INFO] Selected 25 target genomes.
[2024-01-25 20:27:24,486] [INFO] Target genome list was writen to GCF_009827535.1_ASM982753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:24,511] [INFO] Task started: fastANI
[2024-01-25 20:27:24,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfe145ae-3ada-4069-81df-09ccec1c423e/GCF_009827535.1_ASM982753v1_genomic.fna.gz --refList GCF_009827535.1_ASM982753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827535.1_ASM982753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:39,768] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:39,782] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:39,782] [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_009827535.1	s__Altererythrobacter_F oceanensis	100.0	951	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003581645.1	s__Pelagerythrobacter aerophilus	80.4779	472	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.3273	396	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000181515.1	s__Qipengyuania sp000181515	80.2278	458	951	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	80.209	485	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	80.0584	418	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	80.0385	482	951	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	79.9772	421	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	79.8082	445	951	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_900177715.1	s__Erythrobacter xiamenensis	79.7902	465	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	79.6919	420	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993605.1	s__Qipengyuania sp009993605	79.6357	437	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	79.5804	424	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115585.1	s__Qipengyuania nanhaisediminis	79.5774	440	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	79.5391	475	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.5296	436	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762005.1	s__Qipengyuania flava	79.4956	458	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	79.4481	438	951	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	79.4453	400	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003958625.1	s__Tsuneonella rigui	79.4188	423	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	79.3437	380	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.2595	441	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	79.1859	355	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441535.1	s__Tsuneonella troitsensis	79.144	398	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009746585.1	s__Novosphingobium sp009746585	78.7093	325	951	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 20:27:39,784] [INFO] GTDB search result was written to GCF_009827535.1_ASM982753v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:39,784] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:39,788] [INFO] DFAST_QC result json was written to GCF_009827535.1_ASM982753v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:39,788] [INFO] DFAST_QC completed!
[2024-01-25 20:27:39,788] [INFO] Total running time: 0h1m4s