[2024-01-25 18:28:50,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference
[2024-01-25 18:28:51,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,583] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg552112a3-5bc5-4d0a-94a0-124c0ea32d6c/GCF_009857595.1_ASM985759v1_genomic.fna.gz | prodigal -d GCF_009857595.1_ASM985759v1_genomic.fna/cds.fna -a GCF_009857595.1_ASM985759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:29:09,891] [INFO] Task succeeded: Prodigal
[2024-01-25 18:29:09,892] [INFO] Task started: HMMsearch
[2024-01-25 18:29:09,892] [INFO] Running command: hmmsearch --tblout GCF_009857595.1_ASM985759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/reference_markers.hmm GCF_009857595.1_ASM985759v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:29:10,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:29:10,197] [INFO] Found 6/6 markers.
[2024-01-25 18:29:10,250] [INFO] Query marker FASTA was written to GCF_009857595.1_ASM985759v1_genomic.fna/markers.fasta
[2024-01-25 18:29:10,250] [INFO] Task started: Blastn
[2024-01-25 18:29:10,250] [INFO] Running command: blastn -query GCF_009857595.1_ASM985759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/reference_markers.fasta -out GCF_009857595.1_ASM985759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:11,256] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:11,259] [INFO] Selected 20 target genomes.
[2024-01-25 18:29:11,259] [INFO] Target genome list was writen to GCF_009857595.1_ASM985759v1_genomic.fna/target_genomes.txt
[2024-01-25 18:29:11,273] [INFO] Task started: fastANI
[2024-01-25 18:29:11,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg552112a3-5bc5-4d0a-94a0-124c0ea32d6c/GCF_009857595.1_ASM985759v1_genomic.fna.gz --refList GCF_009857595.1_ASM985759v1_genomic.fna/target_genomes.txt --output GCF_009857595.1_ASM985759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:42,853] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:42,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:42,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:42,865] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:29:42,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:42,865] [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
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	100.0	2151	2156	95	conclusive
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	85.8883	1492	2156	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.2167	1301	2156	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.1367	1303	2156	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	83.1326	1187	2156	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	83.0075	1172	2156	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.9871	1161	2156	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	82.9076	1188	2156	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	82.856	1247	2156	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	82.8208	1317	2156	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.7536	1258	2156	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	82.4107	1104	2156	95	below_threshold
Duganella margarita	strain=FT109W	GCA_009857535.1	2692170	2692170	type	True	82.2037	1209	2156	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	81.9616	1163	2156	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	81.9395	1180	2156	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	81.8694	1344	2156	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	81.8552	1182	2156	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.4826	879	2156	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	80.6177	988	2156	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.5872	1080	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:42,867] [INFO] DFAST Taxonomy check result was written to GCF_009857595.1_ASM985759v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:42,868] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:42,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:42,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/checkm_data
[2024-01-25 18:29:42,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:42,933] [INFO] Task started: CheckM
[2024-01-25 18:29:42,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857595.1_ASM985759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857595.1_ASM985759v1_genomic.fna/checkm_input GCF_009857595.1_ASM985759v1_genomic.fna/checkm_result
[2024-01-25 18:30:34,653] [INFO] Task succeeded: CheckM
[2024-01-25 18:30:34,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:30:34,672] [INFO] ===== Completeness check finished =====
[2024-01-25 18:30:34,673] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:30:34,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857595.1_ASM985759v1_genomic.fna/markers.fasta)
[2024-01-25 18:30:34,674] [INFO] Task started: Blastn
[2024-01-25 18:30:34,674] [INFO] Running command: blastn -query GCF_009857595.1_ASM985759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a8a14f6-66a3-4b16-a1a3-c81f65a3f50d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857595.1_ASM985759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:30:36,802] [INFO] Task succeeded: Blastn
[2024-01-25 18:30:36,804] [INFO] Selected 5 target genomes.
[2024-01-25 18:30:36,804] [INFO] Target genome list was writen to GCF_009857595.1_ASM985759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:30:36,811] [INFO] Task started: fastANI
[2024-01-25 18:30:36,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg552112a3-5bc5-4d0a-94a0-124c0ea32d6c/GCF_009857595.1_ASM985759v1_genomic.fna.gz --refList GCF_009857595.1_ASM985759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857595.1_ASM985759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:30:48,004] [INFO] Task succeeded: fastANI
[2024-01-25 18:30:48,009] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:30:48,009] [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_009857595.1	s__Pseudoduganella aquatica_A	100.0	2151	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003053665.1	s__Pseudoduganella sp003053665	90.128	1767	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.77	95.97	0.96	0.89	5	-
GCF_001425265.1	s__Pseudoduganella sp001425265	89.6907	1767	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	89.6868	1795	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116645.1	s__Pseudoduganella namucuonensis	85.8632	1496	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:30:48,010] [INFO] GTDB search result was written to GCF_009857595.1_ASM985759v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:30:48,011] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:30:48,013] [INFO] DFAST_QC result json was written to GCF_009857595.1_ASM985759v1_genomic.fna/dqc_result.json
[2024-01-25 18:30:48,013] [INFO] DFAST_QC completed!
[2024-01-25 18:30:48,013] [INFO] Total running time: 0h1m58s