[2024-01-24 13:47:11,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference
[2024-01-24 13:47:13,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,162] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cae775f-9fda-4d60-bcc9-7eced100a636/GCF_902833725.1_ASM90283372v1_genomic.fna.gz | prodigal -d GCF_902833725.1_ASM90283372v1_genomic.fna/cds.fna -a GCF_902833725.1_ASM90283372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:39,379] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:39,380] [INFO] Task started: HMMsearch
[2024-01-24 13:47:39,380] [INFO] Running command: hmmsearch --tblout GCF_902833725.1_ASM90283372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/reference_markers.hmm GCF_902833725.1_ASM90283372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:39,743] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:39,744] [INFO] Found 6/6 markers.
[2024-01-24 13:47:39,809] [INFO] Query marker FASTA was written to GCF_902833725.1_ASM90283372v1_genomic.fna/markers.fasta
[2024-01-24 13:47:39,810] [INFO] Task started: Blastn
[2024-01-24 13:47:39,810] [INFO] Running command: blastn -query GCF_902833725.1_ASM90283372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/reference_markers.fasta -out GCF_902833725.1_ASM90283372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:40,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:40,869] [INFO] Selected 14 target genomes.
[2024-01-24 13:47:40,869] [INFO] Target genome list was writen to GCF_902833725.1_ASM90283372v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:40,878] [INFO] Task started: fastANI
[2024-01-24 13:47:40,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cae775f-9fda-4d60-bcc9-7eced100a636/GCF_902833725.1_ASM90283372v1_genomic.fna.gz --refList GCF_902833725.1_ASM90283372v1_genomic.fna/target_genomes.txt --output GCF_902833725.1_ASM90283372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:07,555] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:07,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:07,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:07,570] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:48:07,570] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:07,570] [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
Paraburkholderia mimosarum	strain=LMG 23256	GCA_902833725.1	312026	312026	type	True	100.0	2755	2760	95	conclusive
Paraburkholderia mimosarum	strain=LMG 23256	GCA_000472825.1	312026	312026	type	True	99.9574	2638	2760	95	conclusive
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	99.947	2610	2760	95	conclusive
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	88.7301	1822	2760	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	88.5522	1648	2760	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	88.3792	1711	2760	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	88.1785	1519	2760	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	85.1582	1513	2760	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	85.0829	1496	2760	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	85.0596	1452	2760	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	85.015	1458	2760	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.1351	1252	2760	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	80.9773	988	2760	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	80.9378	981	2760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:07,572] [INFO] DFAST Taxonomy check result was written to GCF_902833725.1_ASM90283372v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:07,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:07,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:07,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/checkm_data
[2024-01-24 13:48:07,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:07,651] [INFO] Task started: CheckM
[2024-01-24 13:48:07,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833725.1_ASM90283372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833725.1_ASM90283372v1_genomic.fna/checkm_input GCF_902833725.1_ASM90283372v1_genomic.fna/checkm_result
[2024-01-24 13:49:19,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:19,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,920] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:19,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:19,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833725.1_ASM90283372v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:19,921] [INFO] Task started: Blastn
[2024-01-24 13:49:19,921] [INFO] Running command: blastn -query GCF_902833725.1_ASM90283372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5171940d-1dec-4b87-9c8b-b087ef22bf2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833725.1_ASM90283372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:21,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:21,976] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:21,976] [INFO] Target genome list was writen to GCF_902833725.1_ASM90283372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:21,985] [INFO] Task started: fastANI
[2024-01-24 13:49:21,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cae775f-9fda-4d60-bcc9-7eced100a636/GCF_902833725.1_ASM90283372v1_genomic.fna.gz --refList GCF_902833725.1_ASM90283372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833725.1_ASM90283372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:53,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,089] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:53,089] [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_000739815.1	s__Paraburkholderia mimosarum	99.947	2610	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.63	98.93	0.95	0.86	4	conclusive
GCF_000519185.1	s__Paraburkholderia nodosa	88.7324	1820	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	88.6291	1833	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789655.1	s__Paraburkholderia acidiphila	88.5402	1649	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	88.4268	1834	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739775.1	s__Paraburkholderia heleia	88.4035	1708	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	88.3916	1696	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_904848665.1	s__Paraburkholderia hiiakae	88.3704	1665	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096975.1	s__Paraburkholderia lycopersici	88.216	1514	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268775.1	s__Paraburkholderia unamae	87.8948	1630	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.69	98.69	0.91	0.91	2	-
GCF_000685075.1	s__Paraburkholderia oxyphila	85.0798	1547	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_000785435.2	s__Paraburkholderia sacchari	85.0458	1452	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_000685035.1	s__Paraburkholderia ferrariae	84.7493	1344	2760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:53,098] [INFO] GTDB search result was written to GCF_902833725.1_ASM90283372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:53,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:53,110] [INFO] DFAST_QC result json was written to GCF_902833725.1_ASM90283372v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:53,111] [INFO] DFAST_QC completed!
[2024-01-24 13:49:53,111] [INFO] Total running time: 0h2m41s