[2024-01-24 12:37:23,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:23,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:23,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference
[2024-01-24 12:37:24,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:24,902] [INFO] Task started: Prodigal
[2024-01-24 12:37:24,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg188e1d3d-99a0-4390-b3b0-fd87ad0a29ef/GCF_009674535.1_ASM967453v1_genomic.fna.gz | prodigal -d GCF_009674535.1_ASM967453v1_genomic.fna/cds.fna -a GCF_009674535.1_ASM967453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:50,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:50,388] [INFO] Task started: HMMsearch
[2024-01-24 12:37:50,388] [INFO] Running command: hmmsearch --tblout GCF_009674535.1_ASM967453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/reference_markers.hmm GCF_009674535.1_ASM967453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:50,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:50,747] [INFO] Found 6/6 markers.
[2024-01-24 12:37:50,808] [INFO] Query marker FASTA was written to GCF_009674535.1_ASM967453v1_genomic.fna/markers.fasta
[2024-01-24 12:37:50,809] [INFO] Task started: Blastn
[2024-01-24 12:37:50,809] [INFO] Running command: blastn -query GCF_009674535.1_ASM967453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/reference_markers.fasta -out GCF_009674535.1_ASM967453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:51,677] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:51,680] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:51,681] [INFO] Target genome list was writen to GCF_009674535.1_ASM967453v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:51,687] [INFO] Task started: fastANI
[2024-01-24 12:37:51,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg188e1d3d-99a0-4390-b3b0-fd87ad0a29ef/GCF_009674535.1_ASM967453v1_genomic.fna.gz --refList GCF_009674535.1_ASM967453v1_genomic.fna/target_genomes.txt --output GCF_009674535.1_ASM967453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:15,556] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:15,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:15,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:15,575] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:15,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:15,576] [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 guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	100.0	2484	2485	95	conclusive
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	87.1455	1613	2485	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	87.1146	1622	2485	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	86.6894	1645	2485	95	below_threshold
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	86.547	1645	2485	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	86.3852	1631	2485	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	86.3729	1470	2485	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	85.905	1485	2485	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	85.5928	1616	2485	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	85.5011	1547	2485	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	84.9764	1542	2485	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.2716	1232	2485	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.1024	1110	2485	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.05	1079	2485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:15,579] [INFO] DFAST Taxonomy check result was written to GCF_009674535.1_ASM967453v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:15,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:15,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:15,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/checkm_data
[2024-01-24 12:38:15,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:15,656] [INFO] Task started: CheckM
[2024-01-24 12:38:15,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674535.1_ASM967453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674535.1_ASM967453v1_genomic.fna/checkm_input GCF_009674535.1_ASM967453v1_genomic.fna/checkm_result
[2024-01-24 12:39:27,815] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:27,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:27,837] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:27,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:27,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674535.1_ASM967453v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:27,838] [INFO] Task started: Blastn
[2024-01-24 12:39:27,838] [INFO] Running command: blastn -query GCF_009674535.1_ASM967453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ccb6af-1c44-4954-a022-852567af691f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674535.1_ASM967453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:29,217] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:29,222] [INFO] Selected 15 target genomes.
[2024-01-24 12:39:29,222] [INFO] Target genome list was writen to GCF_009674535.1_ASM967453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:29,233] [INFO] Task started: fastANI
[2024-01-24 12:39:29,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg188e1d3d-99a0-4390-b3b0-fd87ad0a29ef/GCF_009674535.1_ASM967453v1_genomic.fna.gz --refList GCF_009674535.1_ASM967453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674535.1_ASM967453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:55,088] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:55,106] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:55,106] [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_009674535.1	s__Duganella sp009674535	100.0	2484	2485	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_009674565.1	s__Duganella rivi	87.1156	1616	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	87.1129	1622	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_013408245.1	s__Duganella sp013408245	86.97	1569	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720825.1	s__Duganella radicis	86.7221	1641	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857605.1	s__Duganella levis	86.5661	1642	2485	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	86.4875	1631	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.08	98.08	0.91	0.91	2	-
GCF_900109645.1	s__Duganella sp900109645	86.4619	1654	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100205.1	s__Duganella sp900100205	86.23	1644	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009857495.1	s__Duganella sp009857495	86.226	1472	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.63	98.63	0.91	0.91	2	-
GCF_019219065.1	s__Duganella sp019219065	85.9298	1593	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614165.1	s__Duganella callida	85.9103	1485	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857435.1	s__Duganella sp009857435	85.7088	1557	2485	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	85.5838	1618	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143065.1	s__Duganella sacchari	85.4983	1548	2485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.30	97.30	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:55,109] [INFO] GTDB search result was written to GCF_009674535.1_ASM967453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:55,109] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:55,112] [INFO] DFAST_QC result json was written to GCF_009674535.1_ASM967453v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:55,113] [INFO] DFAST_QC completed!
[2024-01-24 12:39:55,113] [INFO] Total running time: 0h2m32s