[2024-01-24 14:31:14,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference
[2024-01-24 14:31:16,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,224] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,225] [INFO] Running command: gunzip -c /var/lib/cwl/stga035c892-3b2d-447a-895e-02b7e97ca3c7/GCF_009828015.1_ASM982801v1_genomic.fna.gz | prodigal -d GCF_009828015.1_ASM982801v1_genomic.fna/cds.fna -a GCF_009828015.1_ASM982801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:26,141] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:26,142] [INFO] Task started: HMMsearch
[2024-01-24 14:31:26,142] [INFO] Running command: hmmsearch --tblout GCF_009828015.1_ASM982801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/reference_markers.hmm GCF_009828015.1_ASM982801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:26,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:26,415] [INFO] Found 6/6 markers.
[2024-01-24 14:31:26,445] [INFO] Query marker FASTA was written to GCF_009828015.1_ASM982801v1_genomic.fna/markers.fasta
[2024-01-24 14:31:26,446] [INFO] Task started: Blastn
[2024-01-24 14:31:26,446] [INFO] Running command: blastn -query GCF_009828015.1_ASM982801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/reference_markers.fasta -out GCF_009828015.1_ASM982801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:27,312] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:27,321] [INFO] Selected 14 target genomes.
[2024-01-24 14:31:27,322] [INFO] Target genome list was writen to GCF_009828015.1_ASM982801v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:27,330] [INFO] Task started: fastANI
[2024-01-24 14:31:27,330] [INFO] Running command: fastANI --query /var/lib/cwl/stga035c892-3b2d-447a-895e-02b7e97ca3c7/GCF_009828015.1_ASM982801v1_genomic.fna.gz --refList GCF_009828015.1_ASM982801v1_genomic.fna/target_genomes.txt --output GCF_009828015.1_ASM982801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:36,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:36,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:36,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:36,719] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:36,720] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:36,720] [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 flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	84.9393	733	997	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	82.0438	623	997	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	81.9374	610	997	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	81.4531	566	997	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	81.3668	587	997	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	81.2832	569	997	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	81.2822	559	997	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	81.2375	583	997	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.2275	567	997	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	81.1279	561	997	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	80.9643	543	997	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	80.7916	468	997	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	80.7829	543	997	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	80.5725	445	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:36,722] [INFO] DFAST Taxonomy check result was written to GCF_009828015.1_ASM982801v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:36,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:36,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:36,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/checkm_data
[2024-01-24 14:31:36,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:36,760] [INFO] Task started: CheckM
[2024-01-24 14:31:36,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828015.1_ASM982801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828015.1_ASM982801v1_genomic.fna/checkm_input GCF_009828015.1_ASM982801v1_genomic.fna/checkm_result
[2024-01-24 14:32:09,079] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:09,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:09,103] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:09,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:09,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828015.1_ASM982801v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:09,105] [INFO] Task started: Blastn
[2024-01-24 14:32:09,105] [INFO] Running command: blastn -query GCF_009828015.1_ASM982801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b612e10-67eb-4093-81cf-1196e4528d55/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828015.1_ASM982801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:10,602] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:10,606] [INFO] Selected 11 target genomes.
[2024-01-24 14:32:10,606] [INFO] Target genome list was writen to GCF_009828015.1_ASM982801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:10,615] [INFO] Task started: fastANI
[2024-01-24 14:32:10,615] [INFO] Running command: fastANI --query /var/lib/cwl/stga035c892-3b2d-447a-895e-02b7e97ca3c7/GCF_009828015.1_ASM982801v1_genomic.fna.gz --refList GCF_009828015.1_ASM982801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828015.1_ASM982801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:18,416] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:18,433] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:18,433] [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_009828015.1	s__Qipengyuania citrea	100.0	991	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.91	97.49	0.87	0.80	20	conclusive
GCA_016764075.1	s__Qipengyuania sp016764075	86.8208	541	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762005.1	s__Qipengyuania flava	84.9393	733	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.04	96.57	0.91	0.85	10	-
GCF_001542855.1	s__Qipengyuania sp001542855	83.5016	656	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_003355455.1	s__Qipengyuania aurea	82.496	650	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.67	97.64	0.83	0.82	3	-
GCF_015767595.1	s__Qipengyuania sp002895025	81.381	584	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.29	96.55	0.87	0.78	16	-
GCF_009827315.1	s__Qipengyuania gaetbuli	81.2263	584	997	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	80.9646	543	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827325.1	s__Qipengyuania vulgaris	80.8366	478	997	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	80.7204	551	997	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	80.555	440	997	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 14:32:18,435] [INFO] GTDB search result was written to GCF_009828015.1_ASM982801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:18,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:18,439] [INFO] DFAST_QC result json was written to GCF_009828015.1_ASM982801v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:18,439] [INFO] DFAST_QC completed!
[2024-01-24 14:32:18,439] [INFO] Total running time: 0h1m4s