[2024-01-25 19:38:50,602] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:50,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:50,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference
[2024-01-25 19:38:51,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:51,822] [INFO] Task started: Prodigal
[2024-01-25 19:38:51,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e6bedab-50f0-409b-aed4-bb6c7c6d6bb3/GCF_014651415.1_ASM1465141v1_genomic.fna.gz | prodigal -d GCF_014651415.1_ASM1465141v1_genomic.fna/cds.fna -a GCF_014651415.1_ASM1465141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:13,002] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:13,002] [INFO] Task started: HMMsearch
[2024-01-25 19:39:13,002] [INFO] Running command: hmmsearch --tblout GCF_014651415.1_ASM1465141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/reference_markers.hmm GCF_014651415.1_ASM1465141v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:13,294] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:13,295] [INFO] Found 6/6 markers.
[2024-01-25 19:39:13,348] [INFO] Query marker FASTA was written to GCF_014651415.1_ASM1465141v1_genomic.fna/markers.fasta
[2024-01-25 19:39:13,348] [INFO] Task started: Blastn
[2024-01-25 19:39:13,348] [INFO] Running command: blastn -query GCF_014651415.1_ASM1465141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/reference_markers.fasta -out GCF_014651415.1_ASM1465141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:14,237] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:14,240] [INFO] Selected 12 target genomes.
[2024-01-25 19:39:14,240] [INFO] Target genome list was writen to GCF_014651415.1_ASM1465141v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:14,261] [INFO] Task started: fastANI
[2024-01-25 19:39:14,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e6bedab-50f0-409b-aed4-bb6c7c6d6bb3/GCF_014651415.1_ASM1465141v1_genomic.fna.gz --refList GCF_014651415.1_ASM1465141v1_genomic.fna/target_genomes.txt --output GCF_014651415.1_ASM1465141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:35,898] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:35,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:35,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:35,907] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:35,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:35,907] [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=KCTC 12343	GCA_014651415.1	321983	321983	type	True	100.0	2439	2440	95	conclusive
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	99.9985	2439	2440	95	conclusive
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	89.7058	1935	2440	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	88.1777	1929	2440	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	87.4978	1755	2440	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	87.4554	1830	2440	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	83.3663	1414	2440	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.2213	1029	2440	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.1818	1038	2440	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.9438	1196	2440	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	80.793	1010	2440	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.3412	972	2440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:35,908] [INFO] DFAST Taxonomy check result was written to GCF_014651415.1_ASM1465141v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:35,909] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:35,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:35,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/checkm_data
[2024-01-25 19:39:35,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:35,978] [INFO] Task started: CheckM
[2024-01-25 19:39:35,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651415.1_ASM1465141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651415.1_ASM1465141v1_genomic.fna/checkm_input GCF_014651415.1_ASM1465141v1_genomic.fna/checkm_result
[2024-01-25 19:40:45,060] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:45,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:45,080] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:45,080] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:45,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651415.1_ASM1465141v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:45,081] [INFO] Task started: Blastn
[2024-01-25 19:40:45,081] [INFO] Running command: blastn -query GCF_014651415.1_ASM1465141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg213a09ce-bd1f-4a82-a637-e21e64a3925a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651415.1_ASM1465141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:46,876] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:46,878] [INFO] Selected 9 target genomes.
[2024-01-25 19:40:46,878] [INFO] Target genome list was writen to GCF_014651415.1_ASM1465141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:46,886] [INFO] Task started: fastANI
[2024-01-25 19:40:46,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e6bedab-50f0-409b-aed4-bb6c7c6d6bb3/GCF_014651415.1_ASM1465141v1_genomic.fna.gz --refList GCF_014651415.1_ASM1465141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651415.1_ASM1465141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:06,507] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:06,514] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:06,514] [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	99.9985	2439	2440	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	89.7278	1932	2440	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	88.1425	1934	2440	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	87.4495	1830	2440	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	84.8258	1632	2440	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	84.6995	1495	2440	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	84.5346	1351	2440	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	83.4322	1374	2440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004421005.1	s__Pseudoduganella plicata	82.8803	1344	2440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:06,515] [INFO] GTDB search result was written to GCF_014651415.1_ASM1465141v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:06,516] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:06,518] [INFO] DFAST_QC result json was written to GCF_014651415.1_ASM1465141v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:06,519] [INFO] DFAST_QC completed!
[2024-01-25 19:41:06,519] [INFO] Total running time: 0h2m16s