[2024-01-25 20:07:50,543] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:50,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:50,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference
[2024-01-25 20:07:51,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:51,655] [INFO] Task started: Prodigal
[2024-01-25 20:07:51,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fffa9b9-452e-40e8-a909-47c948ed02f2/GCF_009720825.1_ASM972082v1_genomic.fna.gz | prodigal -d GCF_009720825.1_ASM972082v1_genomic.fna/cds.fna -a GCF_009720825.1_ASM972082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:12,633] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:12,633] [INFO] Task started: HMMsearch
[2024-01-25 20:08:12,633] [INFO] Running command: hmmsearch --tblout GCF_009720825.1_ASM972082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/reference_markers.hmm GCF_009720825.1_ASM972082v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:12,980] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:12,982] [INFO] Found 6/6 markers.
[2024-01-25 20:08:13,057] [INFO] Query marker FASTA was written to GCF_009720825.1_ASM972082v1_genomic.fna/markers.fasta
[2024-01-25 20:08:13,057] [INFO] Task started: Blastn
[2024-01-25 20:08:13,058] [INFO] Running command: blastn -query GCF_009720825.1_ASM972082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/reference_markers.fasta -out GCF_009720825.1_ASM972082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:14,043] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:14,046] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:14,046] [INFO] Target genome list was writen to GCF_009720825.1_ASM972082v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:14,067] [INFO] Task started: fastANI
[2024-01-25 20:08:14,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fffa9b9-452e-40e8-a909-47c948ed02f2/GCF_009720825.1_ASM972082v1_genomic.fna.gz --refList GCF_009720825.1_ASM972082v1_genomic.fna/target_genomes.txt --output GCF_009720825.1_ASM972082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:39,520] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:39,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:39,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:39,531] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:39,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:39,531] [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
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	100.0	2264	2269	95	conclusive
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	87.8348	1603	2269	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	87.757	1546	2269	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	87.6026	1559	2269	95	below_threshold
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	86.9936	1552	2269	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	86.9549	1560	2269	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	86.778	1425	2269	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	86.7478	1575	2269	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	86.6467	1648	2269	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	86.3753	1476	2269	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	86.3053	1550	2269	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	85.5174	1542	2269	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.7608	1177	2269	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.7429	1258	2269	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	82.7363	1141	2269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:39,533] [INFO] DFAST Taxonomy check result was written to GCF_009720825.1_ASM972082v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:39,533] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:39,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:39,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/checkm_data
[2024-01-25 20:08:39,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:39,627] [INFO] Task started: CheckM
[2024-01-25 20:08:39,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720825.1_ASM972082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720825.1_ASM972082v1_genomic.fna/checkm_input GCF_009720825.1_ASM972082v1_genomic.fna/checkm_result
[2024-01-25 20:09:38,858] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:38,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:38,876] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:38,876] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:38,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720825.1_ASM972082v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:38,877] [INFO] Task started: Blastn
[2024-01-25 20:09:38,878] [INFO] Running command: blastn -query GCF_009720825.1_ASM972082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c2af56-3bfe-4ab8-bf5f-e382671585b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720825.1_ASM972082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:40,881] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:40,884] [INFO] Selected 8 target genomes.
[2024-01-25 20:09:40,884] [INFO] Target genome list was writen to GCF_009720825.1_ASM972082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:40,926] [INFO] Task started: fastANI
[2024-01-25 20:09:40,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fffa9b9-452e-40e8-a909-47c948ed02f2/GCF_009720825.1_ASM972082v1_genomic.fna.gz --refList GCF_009720825.1_ASM972082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720825.1_ASM972082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:55,200] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:55,206] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:55,206] [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_009720825.1	s__Duganella radicis	100.0	2264	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013376005.1	s__Duganella sp013376005	90.2565	1801	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109645.1	s__Duganella sp900109645	89.2155	1703	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857435.1	s__Duganella sp009857435	88.1074	1613	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857445.1	s__Duganella sp009857445	87.835	1603	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674565.1	s__Duganella rivi	87.7892	1543	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_013408245.1	s__Duganella sp013408245	87.4529	1558	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857535.1	s__Duganella margarita	86.9771	1556	2269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:55,207] [INFO] GTDB search result was written to GCF_009720825.1_ASM972082v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:55,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:55,210] [INFO] DFAST_QC result json was written to GCF_009720825.1_ASM972082v1_genomic.fna/dqc_result.json
[2024-01-25 20:09:55,210] [INFO] DFAST_QC completed!
[2024-01-25 20:09:55,210] [INFO] Total running time: 0h2m5s