[2024-01-24 12:13:27,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference
[2024-01-24 12:13:28,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,979] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg91bad66c-b73b-439f-9d3b-658af8b12461/GCF_009857915.1_ASM985791v1_genomic.fna.gz | prodigal -d GCF_009857915.1_ASM985791v1_genomic.fna/cds.fna -a GCF_009857915.1_ASM985791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:45,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:45,055] [INFO] Task started: HMMsearch
[2024-01-24 12:13:45,055] [INFO] Running command: hmmsearch --tblout GCF_009857915.1_ASM985791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/reference_markers.hmm GCF_009857915.1_ASM985791v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:45,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:45,413] [INFO] Found 6/6 markers.
[2024-01-24 12:13:45,456] [INFO] Query marker FASTA was written to GCF_009857915.1_ASM985791v1_genomic.fna/markers.fasta
[2024-01-24 12:13:45,456] [INFO] Task started: Blastn
[2024-01-24 12:13:45,456] [INFO] Running command: blastn -query GCF_009857915.1_ASM985791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/reference_markers.fasta -out GCF_009857915.1_ASM985791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,291] [INFO] Selected 19 target genomes.
[2024-01-24 12:13:46,291] [INFO] Target genome list was writen to GCF_009857915.1_ASM985791v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:46,300] [INFO] Task started: fastANI
[2024-01-24 12:13:46,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg91bad66c-b73b-439f-9d3b-658af8b12461/GCF_009857915.1_ASM985791v1_genomic.fna.gz --refList GCF_009857915.1_ASM985791v1_genomic.fna/target_genomes.txt --output GCF_009857915.1_ASM985791v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,030] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,051] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:12,051] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:12,051] [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
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.031	1180	1730	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	82.9506	1190	1730	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	82.258	1081	1730	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.1602	1099	1730	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	82.1225	1094	1730	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	82.0908	1040	1730	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	82.03	1006	1730	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	81.9482	1062	1730	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	81.9435	1070	1730	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.9152	976	1730	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	81.7909	1037	1730	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.7626	968	1730	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	81.7609	979	1730	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	81.7471	1091	1730	95	below_threshold
Duganella levis	strain=CY42W	GCA_009857605.1	2692169	2692169	type	True	81.7367	1054	1730	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	81.7076	971	1730	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	81.1262	945	1730	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	80.9488	929	1730	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	79.7787	738	1730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,053] [INFO] DFAST Taxonomy check result was written to GCF_009857915.1_ASM985791v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,054] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,054] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/checkm_data
[2024-01-24 12:14:12,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,111] [INFO] Task started: CheckM
[2024-01-24 12:14:12,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857915.1_ASM985791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857915.1_ASM985791v1_genomic.fna/checkm_input GCF_009857915.1_ASM985791v1_genomic.fna/checkm_result
[2024-01-24 12:14:59,910] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:59,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,933] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:59,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:59,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857915.1_ASM985791v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:59,934] [INFO] Task started: Blastn
[2024-01-24 12:14:59,934] [INFO] Running command: blastn -query GCF_009857915.1_ASM985791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d5c64e-73d7-45a1-9670-c6259d403117/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857915.1_ASM985791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:01,247] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:01,252] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:01,253] [INFO] Target genome list was writen to GCF_009857915.1_ASM985791v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:01,264] [INFO] Task started: fastANI
[2024-01-24 12:15:01,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg91bad66c-b73b-439f-9d3b-658af8b12461/GCF_009857915.1_ASM985791v1_genomic.fna.gz --refList GCF_009857915.1_ASM985791v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857915.1_ASM985791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:18,694] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:18,709] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:18,710] [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_009857915.1	s__Duganella sp009857915	100.0	1730	1730	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_009857835.1	s__Duganella fentianensis	89.5957	1428	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720775.1	s__Duganella danionis	89.0129	1454	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380215.1	s__Duganella sp009380215	82.9649	1187	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335815.1	s__Duganella sp000335815	82.8935	1213	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	-
GCF_003416895.1	s__Duganella sp003416895	82.8506	1190	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCA_000381565.1	s__Duganella sp000381565	82.7853	1186	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_013375995.1	s__Duganella sp013375995	82.7695	1133	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674495.1	s__Duganella alba	82.1765	1097	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_900143065.1	s__Duganella sacchari	81.9474	1069	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.30	97.30	0.91	0.91	2	-
GCF_019219065.1	s__Duganella sp019219065	81.8187	1029	1730	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	81.6133	1024	1730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,713] [INFO] GTDB search result was written to GCF_009857915.1_ASM985791v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:18,715] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:18,731] [INFO] DFAST_QC result json was written to GCF_009857915.1_ASM985791v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:18,731] [INFO] DFAST_QC completed!
[2024-01-24 12:15:18,731] [INFO] Total running time: 0h1m51s