[2024-01-24 13:21:10,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference
[2024-01-24 13:21:12,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,319] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dd3746e-5bb0-496a-8aae-b2c2a984ccd6/GCF_014191875.1_ASM1419187v1_genomic.fna.gz | prodigal -d GCF_014191875.1_ASM1419187v1_genomic.fna/cds.fna -a GCF_014191875.1_ASM1419187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:32,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:32,962] [INFO] Task started: HMMsearch
[2024-01-24 13:21:32,962] [INFO] Running command: hmmsearch --tblout GCF_014191875.1_ASM1419187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/reference_markers.hmm GCF_014191875.1_ASM1419187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:33,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:33,319] [INFO] Found 6/6 markers.
[2024-01-24 13:21:33,384] [INFO] Query marker FASTA was written to GCF_014191875.1_ASM1419187v1_genomic.fna/markers.fasta
[2024-01-24 13:21:33,385] [INFO] Task started: Blastn
[2024-01-24 13:21:33,385] [INFO] Running command: blastn -query GCF_014191875.1_ASM1419187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/reference_markers.fasta -out GCF_014191875.1_ASM1419187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:34,437] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:34,442] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:34,443] [INFO] Target genome list was writen to GCF_014191875.1_ASM1419187v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:34,452] [INFO] Task started: fastANI
[2024-01-24 13:21:34,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd3746e-5bb0-496a-8aae-b2c2a984ccd6/GCF_014191875.1_ASM1419187v1_genomic.fna.gz --refList GCF_014191875.1_ASM1419187v1_genomic.fna/target_genomes.txt --output GCF_014191875.1_ASM1419187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:01,442] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:01,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:01,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:01,456] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:01,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:01,456] [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 violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	100.0	2055	2057	95	conclusive
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	82.9871	1173	2057	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	82.6523	1181	2057	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	82.4373	1047	2057	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	82.3277	1040	2057	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	82.2416	1037	2057	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.1782	1063	2057	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	82.0986	1075	2057	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	82.0384	1079	2057	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	82.035	1044	2057	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	81.9944	1067	2057	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	81.9047	1112	2057	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	81.1953	1003	2057	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	81.0965	923	2057	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	80.9718	1024	2057	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.9206	759	2057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:01,459] [INFO] DFAST Taxonomy check result was written to GCF_014191875.1_ASM1419187v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:01,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:01,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:01,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/checkm_data
[2024-01-24 13:22:01,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:01,539] [INFO] Task started: CheckM
[2024-01-24 13:22:01,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191875.1_ASM1419187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191875.1_ASM1419187v1_genomic.fna/checkm_input GCF_014191875.1_ASM1419187v1_genomic.fna/checkm_result
[2024-01-24 13:23:00,055] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:00,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:00,089] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:00,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:00,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191875.1_ASM1419187v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:00,090] [INFO] Task started: Blastn
[2024-01-24 13:23:00,090] [INFO] Running command: blastn -query GCF_014191875.1_ASM1419187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc09c0727-169c-4c4d-ac21-804914f340b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191875.1_ASM1419187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:02,191] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:02,195] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:02,195] [INFO] Target genome list was writen to GCF_014191875.1_ASM1419187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:02,207] [INFO] Task started: fastANI
[2024-01-24 13:23:02,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd3746e-5bb0-496a-8aae-b2c2a984ccd6/GCF_014191875.1_ASM1419187v1_genomic.fna.gz --refList GCF_014191875.1_ASM1419187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191875.1_ASM1419187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:26,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:26,594] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:26,594] [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_014191875.1	s__Pseudoduganella violacea	100.0	2055	2057	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_001191005.1	s__Pseudoduganella sp001191005	93.7106	1832	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	93.4044	1757	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053665.1	s__Pseudoduganella sp003053665	83.0227	1193	2057	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	82.7799	1229	2057	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	82.6972	1238	2057	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	82.6358	1183	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425385.1	s__Pseudoduganella violaceinigra	82.2128	1114	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	82.0179	1083	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028855.1	s__Pseudoduganella armeniaca	81.9025	1114	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008011715.1	s__Pseudoduganella haloabium	81.8802	1120	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_009674485.1	s__Pseudoduganella sp009674485	80.9572	1026	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	80.9184	759	2057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:26,596] [INFO] GTDB search result was written to GCF_014191875.1_ASM1419187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:26,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:26,602] [INFO] DFAST_QC result json was written to GCF_014191875.1_ASM1419187v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:26,602] [INFO] DFAST_QC completed!
[2024-01-24 13:23:26,602] [INFO] Total running time: 0h2m16s