[2024-01-24 11:51:06,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,938] [INFO] DQC Reference Directory: /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference
[2024-01-24 11:51:08,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,201] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,202] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c57eab5-b7b0-4767-b0b7-d57ec4e82def/GCF_001758785.1_ASM175878v1_genomic.fna.gz | prodigal -d GCF_001758785.1_ASM175878v1_genomic.fna/cds.fna -a GCF_001758785.1_ASM175878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:27,921] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:27,922] [INFO] Task started: HMMsearch
[2024-01-24 11:51:27,922] [INFO] Running command: hmmsearch --tblout GCF_001758785.1_ASM175878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/reference_markers.hmm GCF_001758785.1_ASM175878v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:28,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:28,333] [INFO] Found 6/6 markers.
[2024-01-24 11:51:28,382] [INFO] Query marker FASTA was written to GCF_001758785.1_ASM175878v1_genomic.fna/markers.fasta
[2024-01-24 11:51:28,383] [INFO] Task started: Blastn
[2024-01-24 11:51:28,383] [INFO] Running command: blastn -query GCF_001758785.1_ASM175878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/reference_markers.fasta -out GCF_001758785.1_ASM175878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:29,389] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:29,393] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:29,393] [INFO] Target genome list was writen to GCF_001758785.1_ASM175878v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:29,412] [INFO] Task started: fastANI
[2024-01-24 11:51:29,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c57eab5-b7b0-4767-b0b7-d57ec4e82def/GCF_001758785.1_ASM175878v1_genomic.fna.gz --refList GCF_001758785.1_ASM175878v1_genomic.fna/target_genomes.txt --output GCF_001758785.1_ASM175878v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,098] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,114] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:46,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:46,114] [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 phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	100.0	1972	1980	95	conclusive
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.7132	1214	1980	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	83.6899	1263	1980	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	83.634	1239	1980	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.5914	1222	1980	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	83.5765	1286	1980	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	82.8771	1265	1980	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	82.7709	1214	1980	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.4985	1015	1980	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.1194	1002	1980	95	below_threshold
Duganella flavida	strain=FT135W	GCA_009857445.1	2692175	2692175	type	True	81.9088	1150	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,186] [INFO] DFAST Taxonomy check result was written to GCF_001758785.1_ASM175878v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/checkm_data
[2024-01-24 11:51:46,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,254] [INFO] Task started: CheckM
[2024-01-24 11:51:46,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001758785.1_ASM175878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001758785.1_ASM175878v1_genomic.fna/checkm_input GCF_001758785.1_ASM175878v1_genomic.fna/checkm_result
[2024-01-24 11:52:42,551] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:42,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:42,580] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:42,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:42,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001758785.1_ASM175878v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:42,582] [INFO] Task started: Blastn
[2024-01-24 11:52:42,582] [INFO] Running command: blastn -query GCF_001758785.1_ASM175878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga47aa5a4-2841-4055-a936-ea59f6218673/dqc_reference/reference_markers_gtdb.fasta -out GCF_001758785.1_ASM175878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:44,509] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:44,513] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:44,513] [INFO] Target genome list was writen to GCF_001758785.1_ASM175878v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:44,551] [INFO] Task started: fastANI
[2024-01-24 11:52:44,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c57eab5-b7b0-4767-b0b7-d57ec4e82def/GCF_001758785.1_ASM175878v1_genomic.fna.gz --refList GCF_001758785.1_ASM175878v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001758785.1_ASM175878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:03,669] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:03,685] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:03,685] [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_001758785.1	s__Duganella phyllosphaerae	100.0	1972	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000383895.1	s__Duganella zoogloeoides	90.652	1685	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	96.93	95.29	0.93	0.88	4	-
GCF_001423125.1	s__Duganella sp001423125	88.0742	1453	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110275.1	s__Duganella sp900110275	83.9886	1399	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833525.1	s__Duganella sp017833525	83.9586	1427	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416985.1	s__Duganella sp003416985	83.8669	1256	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_009674565.1	s__Duganella rivi	83.6944	1261	1980	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	83.6267	1239	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	100.00	100.00	1.00	1.00	2	-
GCF_011090165.1	s__Duganella aceris	83.615	1281	1980	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	83.5537	1227	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	83.1175	1278	1980	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	82.8684	1224	1980	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:03,687] [INFO] GTDB search result was written to GCF_001758785.1_ASM175878v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:03,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:03,690] [INFO] DFAST_QC result json was written to GCF_001758785.1_ASM175878v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:03,691] [INFO] DFAST_QC completed!
[2024-01-24 11:53:03,691] [INFO] Total running time: 0h1m57s