[2024-01-24 12:23:34,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:34,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:34,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference
[2024-01-24 12:23:36,345] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,346] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e719b31-3704-42a4-b311-d1713e1d720c/GCF_004322755.1_ASM432275v1_genomic.fna.gz | prodigal -d GCF_004322755.1_ASM432275v1_genomic.fna/cds.fna -a GCF_004322755.1_ASM432275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:02,090] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:02,091] [INFO] Task started: HMMsearch
[2024-01-24 12:24:02,091] [INFO] Running command: hmmsearch --tblout GCF_004322755.1_ASM432275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/reference_markers.hmm GCF_004322755.1_ASM432275v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:02,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:02,380] [INFO] Found 6/6 markers.
[2024-01-24 12:24:02,432] [INFO] Query marker FASTA was written to GCF_004322755.1_ASM432275v1_genomic.fna/markers.fasta
[2024-01-24 12:24:02,432] [INFO] Task started: Blastn
[2024-01-24 12:24:02,432] [INFO] Running command: blastn -query GCF_004322755.1_ASM432275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/reference_markers.fasta -out GCF_004322755.1_ASM432275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,462] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,465] [INFO] Selected 12 target genomes.
[2024-01-24 12:24:03,465] [INFO] Target genome list was writen to GCF_004322755.1_ASM432275v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:03,470] [INFO] Task started: fastANI
[2024-01-24 12:24:03,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e719b31-3704-42a4-b311-d1713e1d720c/GCF_004322755.1_ASM432275v1_genomic.fna.gz --refList GCF_004322755.1_ASM432275v1_genomic.fna/target_genomes.txt --output GCF_004322755.1_ASM432275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:24,688] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:24,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:24,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:24,699] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:24:24,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:24,699] [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 albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	100.0	2479	2479	95	conclusive
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	99.9805	2438	2479	95	conclusive
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	89.7325	1947	2479	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	88.158	1927	2479	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	87.5461	1830	2479	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	87.5061	1757	2479	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	84.9325	1622	2479	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.2494	1040	2479	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.1786	1030	2479	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.072	1201	2479	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	80.8209	1013	2479	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.3471	982	2479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:24,701] [INFO] DFAST Taxonomy check result was written to GCF_004322755.1_ASM432275v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:24,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:24,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:24,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/checkm_data
[2024-01-24 12:24:24,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:24,770] [INFO] Task started: CheckM
[2024-01-24 12:24:24,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004322755.1_ASM432275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004322755.1_ASM432275v1_genomic.fna/checkm_input GCF_004322755.1_ASM432275v1_genomic.fna/checkm_result
[2024-01-24 12:25:52,524] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:52,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:52,544] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:52,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:52,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004322755.1_ASM432275v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:52,545] [INFO] Task started: Blastn
[2024-01-24 12:25:52,545] [INFO] Running command: blastn -query GCF_004322755.1_ASM432275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c8dfb3-ec14-4339-83b4-34b005fdf649/dqc_reference/reference_markers_gtdb.fasta -out GCF_004322755.1_ASM432275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:54,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:54,536] [INFO] Selected 8 target genomes.
[2024-01-24 12:25:54,536] [INFO] Target genome list was writen to GCF_004322755.1_ASM432275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:54,541] [INFO] Task started: fastANI
[2024-01-24 12:25:54,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e719b31-3704-42a4-b311-d1713e1d720c/GCF_004322755.1_ASM432275v1_genomic.fna.gz --refList GCF_004322755.1_ASM432275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004322755.1_ASM432275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:10,171] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:10,179] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:10,179] [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_004322755.1	s__Pseudoduganella albidiflava	100.0	2479	2479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014192225.1	s__Pseudoduganella umbonata	89.7263	1948	2479	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	88.1771	1924	2479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009727155.1	s__Pseudoduganella dura	87.5158	1836	2479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830495.1	s__Pseudoduganella flava	84.9038	1626	2479	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	84.8157	1500	2479	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	84.4233	1383	2479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004421005.1	s__Pseudoduganella plicata	83.148	1330	2479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:10,180] [INFO] GTDB search result was written to GCF_004322755.1_ASM432275v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:10,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:10,184] [INFO] DFAST_QC result json was written to GCF_004322755.1_ASM432275v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:10,184] [INFO] DFAST_QC completed!
[2024-01-24 12:26:10,184] [INFO] Total running time: 0h2m35s