[2024-01-24 11:26:20,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,973] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference
[2024-01-24 11:26:22,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,186] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,186] [INFO] Running command: gunzip -c /var/lib/cwl/stg78cfef42-9316-4713-ad1b-813e7adbf30d/GCF_019711615.1_ASM1971161v1_genomic.fna.gz | prodigal -d GCF_019711615.1_ASM1971161v1_genomic.fna/cds.fna -a GCF_019711615.1_ASM1971161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:30,320] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:30,321] [INFO] Task started: HMMsearch
[2024-01-24 11:26:30,321] [INFO] Running command: hmmsearch --tblout GCF_019711615.1_ASM1971161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/reference_markers.hmm GCF_019711615.1_ASM1971161v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:30,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:30,621] [INFO] Found 6/6 markers.
[2024-01-24 11:26:30,650] [INFO] Query marker FASTA was written to GCF_019711615.1_ASM1971161v1_genomic.fna/markers.fasta
[2024-01-24 11:26:30,650] [INFO] Task started: Blastn
[2024-01-24 11:26:30,650] [INFO] Running command: blastn -query GCF_019711615.1_ASM1971161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/reference_markers.fasta -out GCF_019711615.1_ASM1971161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:31,539] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:31,542] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:31,542] [INFO] Target genome list was writen to GCF_019711615.1_ASM1971161v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:31,547] [INFO] Task started: fastANI
[2024-01-24 11:26:31,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg78cfef42-9316-4713-ad1b-813e7adbf30d/GCF_019711615.1_ASM1971161v1_genomic.fna.gz --refList GCF_019711615.1_ASM1971161v1_genomic.fna/target_genomes.txt --output GCF_019711615.1_ASM1971161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,382] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,397] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:38,397] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:38,397] [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 intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	100.0	897	897	95	conclusive
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	91.2792	808	897	95	below_threshold
Qipengyuania aquimaris	strain=JCM 12189	GCA_009827445.1	255984	255984	suspected-type	True	90.3798	776	897	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	88.8564	789	897	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	83.2259	661	897	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	82.2888	603	897	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	82.1778	595	897	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	82.0649	618	897	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	81.9843	605	897	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	81.545	557	897	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	81.1375	571	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,399] [INFO] DFAST Taxonomy check result was written to GCF_019711615.1_ASM1971161v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/checkm_data
[2024-01-24 11:26:38,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,434] [INFO] Task started: CheckM
[2024-01-24 11:26:38,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019711615.1_ASM1971161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019711615.1_ASM1971161v1_genomic.fna/checkm_input GCF_019711615.1_ASM1971161v1_genomic.fna/checkm_result
[2024-01-24 11:27:07,210] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:07,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:07,231] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:07,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:07,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019711615.1_ASM1971161v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:07,233] [INFO] Task started: Blastn
[2024-01-24 11:27:07,233] [INFO] Running command: blastn -query GCF_019711615.1_ASM1971161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb97dcc6-a898-4f07-a230-93c029aa4e1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019711615.1_ASM1971161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:08,889] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:08,893] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:08,893] [INFO] Target genome list was writen to GCF_019711615.1_ASM1971161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:08,903] [INFO] Task started: fastANI
[2024-01-24 11:27:08,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg78cfef42-9316-4713-ad1b-813e7adbf30d/GCF_019711615.1_ASM1971161v1_genomic.fna.gz --refList GCF_019711615.1_ASM1971161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019711615.1_ASM1971161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:14,793] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:14,805] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:14,805] [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	91.2792	808	897	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827445.1	s__Qipengyuania aquimaris	90.3798	776	897	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	88.8564	789	897	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	83.216	662	897	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	81.8995	585	897	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	81.6043	594	897	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	81.5775	474	897	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	80.8231	407	897	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695185.1	s__Qipengyuania sp002695185	80.1228	388	897	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	96.33	96.22	0.77	0.72	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,807] [INFO] GTDB search result was written to GCF_019711615.1_ASM1971161v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:14,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:14,810] [INFO] DFAST_QC result json was written to GCF_019711615.1_ASM1971161v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:14,810] [INFO] DFAST_QC completed!
[2024-01-24 11:27:14,810] [INFO] Total running time: 0h0m54s