[2024-01-24 14:05:15,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:15,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:15,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference
[2024-01-24 14:05:17,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,207] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8a2534b-9892-4d39-9d55-4773a192e179/GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/cds.fna -a GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:25,953] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:25,954] [INFO] Task started: HMMsearch
[2024-01-24 14:05:25,954] [INFO] Running command: hmmsearch --tblout GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/reference_markers.hmm GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:26,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:26,214] [INFO] Found 6/6 markers.
[2024-01-24 14:05:26,255] [INFO] Query marker FASTA was written to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:26,256] [INFO] Task started: Blastn
[2024-01-24 14:05:26,256] [INFO] Running command: blastn -query GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/reference_markers.fasta -out GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:27,237] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:27,240] [INFO] Selected 12 target genomes.
[2024-01-24 14:05:27,240] [INFO] Target genome list was writen to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:27,245] [INFO] Task started: fastANI
[2024-01-24 14:05:27,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a2534b-9892-4d39-9d55-4773a192e179/GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna.gz --refList GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:35,199] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:35,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:35,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:35,214] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:35,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:35,214] [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	100.0	960	960	95	conclusive
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	92.7975	814	960	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	91.2814	795	960	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	89.2823	800	960	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	82.988	666	960	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	82.1807	627	960	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	82.1079	616	960	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	82.1035	623	960	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	82.0797	619	960	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.5606	570	960	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.4228	555	960	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	80.1628	471	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:35,216] [INFO] DFAST Taxonomy check result was written to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:35,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:35,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:35,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/checkm_data
[2024-01-24 14:05:35,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:35,249] [INFO] Task started: CheckM
[2024-01-24 14:05:35,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/checkm_input GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:05,340] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:05,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:05,406] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:05,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:05,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:05,408] [INFO] Task started: Blastn
[2024-01-24 14:06:05,408] [INFO] Running command: blastn -query GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a4dd42c-e3ba-469e-878c-d2bf94d2e892/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:07,150] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:07,159] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:07,159] [INFO] Target genome list was writen to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:07,169] [INFO] Task started: fastANI
[2024-01-24 14:06:07,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8a2534b-9892-4d39-9d55-4773a192e179/GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna.gz --refList GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:13,929] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:13,944] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:13,945] [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_900115585.1	s__Qipengyuania nanhaisediminis	100.0	960	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827445.1	s__Qipengyuania aquimaris	92.7978	814	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	89.2823	800	960	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	82.988	666	960	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	81.8986	607	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	81.8307	570	960	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	81.5952	483	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	80.7944	426	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828015.1	s__Qipengyuania citrea	80.6961	538	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	-
GCA_003248395.1	s__Qipengyuania sp003248395	80.2405	426	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	79.2649	344	960	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:13,946] [INFO] GTDB search result was written to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:13,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:13,950] [INFO] DFAST_QC result json was written to GCF_900115585.1_IMG-taxon_2619618819_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:13,950] [INFO] DFAST_QC completed!
[2024-01-24 14:06:13,950] [INFO] Total running time: 0h0m58s