[2024-01-24 11:59:22,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,960] [INFO] DQC Reference Directory: /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference
[2024-01-24 11:59:25,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,645] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,646] [INFO] Running command: gunzip -c /var/lib/cwl/stga7abde44-cfc2-4447-84b9-f63c30a2a86a/GCF_009827445.1_ASM982744v1_genomic.fna.gz | prodigal -d GCF_009827445.1_ASM982744v1_genomic.fna/cds.fna -a GCF_009827445.1_ASM982744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:33,739] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:33,740] [INFO] Task started: HMMsearch
[2024-01-24 11:59:33,740] [INFO] Running command: hmmsearch --tblout GCF_009827445.1_ASM982744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/reference_markers.hmm GCF_009827445.1_ASM982744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:33,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:33,995] [INFO] Found 6/6 markers.
[2024-01-24 11:59:34,023] [INFO] Query marker FASTA was written to GCF_009827445.1_ASM982744v1_genomic.fna/markers.fasta
[2024-01-24 11:59:34,024] [INFO] Task started: Blastn
[2024-01-24 11:59:34,024] [INFO] Running command: blastn -query GCF_009827445.1_ASM982744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/reference_markers.fasta -out GCF_009827445.1_ASM982744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:34,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:34,897] [INFO] Selected 9 target genomes.
[2024-01-24 11:59:34,897] [INFO] Target genome list was writen to GCF_009827445.1_ASM982744v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:34,919] [INFO] Task started: fastANI
[2024-01-24 11:59:34,920] [INFO] Running command: fastANI --query /var/lib/cwl/stga7abde44-cfc2-4447-84b9-f63c30a2a86a/GCF_009827445.1_ASM982744v1_genomic.fna.gz --refList GCF_009827445.1_ASM982744v1_genomic.fna/target_genomes.txt --output GCF_009827445.1_ASM982744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:40,683] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:40,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:40,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:40,692] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:40,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:40,693] [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 aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	100.0	887	887	95	conclusive
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	92.7961	813	887	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	90.4607	774	887	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	89.4721	766	887	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	82.6016	662	887	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	81.8755	601	887	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	81.8658	593	887	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	81.8625	591	887	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	81.6868	582	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:40,696] [INFO] DFAST Taxonomy check result was written to GCF_009827445.1_ASM982744v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:40,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:40,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:40,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/checkm_data
[2024-01-24 11:59:40,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:40,728] [INFO] Task started: CheckM
[2024-01-24 11:59:40,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827445.1_ASM982744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827445.1_ASM982744v1_genomic.fna/checkm_input GCF_009827445.1_ASM982744v1_genomic.fna/checkm_result
[2024-01-24 12:00:08,449] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:08,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:08,473] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:08,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:08,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827445.1_ASM982744v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:08,474] [INFO] Task started: Blastn
[2024-01-24 12:00:08,474] [INFO] Running command: blastn -query GCF_009827445.1_ASM982744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5417714-9e41-465b-9545-1047fdfce0af/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827445.1_ASM982744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:10,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:10,108] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:10,108] [INFO] Target genome list was writen to GCF_009827445.1_ASM982744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:10,116] [INFO] Task started: fastANI
[2024-01-24 12:00:10,116] [INFO] Running command: fastANI --query /var/lib/cwl/stga7abde44-cfc2-4447-84b9-f63c30a2a86a/GCF_009827445.1_ASM982744v1_genomic.fna.gz --refList GCF_009827445.1_ASM982744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827445.1_ASM982744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:15,503] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:15,513] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:15,514] [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_009827445.1	s__Qipengyuania aquimaris	100.0	887	887	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_900115585.1	s__Qipengyuania nanhaisediminis	92.7961	813	887	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	89.4677	767	887	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	82.6138	661	887	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	81.6369	561	887	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	81.5097	469	887	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	81.3704	588	887	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	80.6941	378	887	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	80.003	510	887	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 12:00:15,515] [INFO] GTDB search result was written to GCF_009827445.1_ASM982744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:15,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:15,518] [INFO] DFAST_QC result json was written to GCF_009827445.1_ASM982744v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:15,518] [INFO] DFAST_QC completed!
[2024-01-24 12:00:15,518] [INFO] Total running time: 0h0m53s