[2024-01-24 12:47:08,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:08,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:08,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference
[2024-01-24 12:47:10,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:10,117] [INFO] Task started: Prodigal
[2024-01-24 12:47:10,117] [INFO] Running command: gunzip -c /var/lib/cwl/stg579ceb97-ad95-4dc5-8bfc-f8a54da33de2/GCF_009727155.1_ASM972715v1_genomic.fna.gz | prodigal -d GCF_009727155.1_ASM972715v1_genomic.fna/cds.fna -a GCF_009727155.1_ASM972715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:32,951] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:32,951] [INFO] Task started: HMMsearch
[2024-01-24 12:47:32,951] [INFO] Running command: hmmsearch --tblout GCF_009727155.1_ASM972715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/reference_markers.hmm GCF_009727155.1_ASM972715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:33,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:33,377] [INFO] Found 6/6 markers.
[2024-01-24 12:47:33,433] [INFO] Query marker FASTA was written to GCF_009727155.1_ASM972715v1_genomic.fna/markers.fasta
[2024-01-24 12:47:33,434] [INFO] Task started: Blastn
[2024-01-24 12:47:33,434] [INFO] Running command: blastn -query GCF_009727155.1_ASM972715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/reference_markers.fasta -out GCF_009727155.1_ASM972715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:34,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:34,564] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:34,565] [INFO] Target genome list was writen to GCF_009727155.1_ASM972715v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:34,570] [INFO] Task started: fastANI
[2024-01-24 12:47:34,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg579ceb97-ad95-4dc5-8bfc-f8a54da33de2/GCF_009727155.1_ASM972715v1_genomic.fna.gz --refList GCF_009727155.1_ASM972715v1_genomic.fna/target_genomes.txt --output GCF_009727155.1_ASM972715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:58,015] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:58,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:58,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:58,032] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:58,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:58,033] [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 dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	100.0	2316	2316	95	conclusive
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	99.9609	2227	2316	95	conclusive
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	87.6758	1792	2316	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	87.543	1788	2316	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	87.4863	1788	2316	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	87.2867	1825	2316	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	84.9624	1493	2316	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	83.3503	1356	2316	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.117	998	2316	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.0305	1190	2316	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	80.8157	974	2316	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.3988	857	2316	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.3123	924	2316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:58,035] [INFO] DFAST Taxonomy check result was written to GCF_009727155.1_ASM972715v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:58,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:58,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:58,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/checkm_data
[2024-01-24 12:47:58,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:58,112] [INFO] Task started: CheckM
[2024-01-24 12:47:58,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009727155.1_ASM972715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009727155.1_ASM972715v1_genomic.fna/checkm_input GCF_009727155.1_ASM972715v1_genomic.fna/checkm_result
[2024-01-24 12:49:17,055] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:17,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:17,075] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:17,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:17,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009727155.1_ASM972715v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:17,076] [INFO] Task started: Blastn
[2024-01-24 12:49:17,076] [INFO] Running command: blastn -query GCF_009727155.1_ASM972715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc503bbf1-f6a0-41ac-bc46-9a43cfa609aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_009727155.1_ASM972715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:19,261] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:19,265] [INFO] Selected 8 target genomes.
[2024-01-24 12:49:19,265] [INFO] Target genome list was writen to GCF_009727155.1_ASM972715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:19,272] [INFO] Task started: fastANI
[2024-01-24 12:49:19,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg579ceb97-ad95-4dc5-8bfc-f8a54da33de2/GCF_009727155.1_ASM972715v1_genomic.fna.gz --refList GCF_009727155.1_ASM972715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009727155.1_ASM972715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:34,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:34,302] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:34,302] [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_009727155.1	s__Pseudoduganella dura	100.0	2316	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004322755.1	s__Pseudoduganella albidiflava	87.6757	1792	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192225.1	s__Pseudoduganella umbonata	87.5024	1786	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	87.3068	1822	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830495.1	s__Pseudoduganella flava	85.2017	1547	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830455.1	s__Pseudoduganella lurida	84.9717	1491	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454505.1	s__Pseudoduganella sp002454505	84.6866	1349	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720835.1	s__Pseudoduganella buxea	83.3911	1349	2316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:34,305] [INFO] GTDB search result was written to GCF_009727155.1_ASM972715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:34,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:34,310] [INFO] DFAST_QC result json was written to GCF_009727155.1_ASM972715v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:34,310] [INFO] DFAST_QC completed!
[2024-01-24 12:49:34,310] [INFO] Total running time: 0h2m25s