[2024-01-24 13:46:03,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference
[2024-01-24 13:46:04,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:04,947] [INFO] Task started: Prodigal
[2024-01-24 13:46:04,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ac3548f-53e8-4a0c-a6ab-af36fef832f3/GCF_000685035.1_ASM68503v1_genomic.fna.gz | prodigal -d GCF_000685035.1_ASM68503v1_genomic.fna/cds.fna -a GCF_000685035.1_ASM68503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:29,608] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:29,609] [INFO] Task started: HMMsearch
[2024-01-24 13:46:29,609] [INFO] Running command: hmmsearch --tblout GCF_000685035.1_ASM68503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/reference_markers.hmm GCF_000685035.1_ASM68503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:29,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:29,997] [INFO] Found 6/6 markers.
[2024-01-24 13:46:30,059] [INFO] Query marker FASTA was written to GCF_000685035.1_ASM68503v1_genomic.fna/markers.fasta
[2024-01-24 13:46:30,060] [INFO] Task started: Blastn
[2024-01-24 13:46:30,060] [INFO] Running command: blastn -query GCF_000685035.1_ASM68503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/reference_markers.fasta -out GCF_000685035.1_ASM68503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:31,145] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:31,149] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:31,149] [INFO] Target genome list was writen to GCF_000685035.1_ASM68503v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:31,164] [INFO] Task started: fastANI
[2024-01-24 13:46:31,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac3548f-53e8-4a0c-a6ab-af36fef832f3/GCF_000685035.1_ASM68503v1_genomic.fna.gz --refList GCF_000685035.1_ASM68503v1_genomic.fna/target_genomes.txt --output GCF_000685035.1_ASM68503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:09,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:09,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:09,959] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:09,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:09,959] [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 ferrariae	strain=NBRC 106233	GCA_000685035.1	386056	386056	type	True	100.0	2597	2602	95	conclusive
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	87.3123	1448	2602	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	85.1961	1373	2602	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	85.0624	1457	2602	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	85.0424	1463	2602	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	85.0353	1444	2602	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	85.0224	1412	2602	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	84.9578	1462	2602	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	84.9029	1403	2602	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	84.8593	1401	2602	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	84.8367	1281	2602	95	below_threshold
Paraburkholderia dinghuensis	strain=DHOA04	GCA_003837865.1	2305225	2305225	type	True	84.7845	1149	2602	95	below_threshold
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	84.7004	1321	2602	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	84.6701	1395	2602	95	below_threshold
Paraburkholderia hiiakae	strain=LMG 27952	GCA_904848665.1	1081782	1081782	type	True	84.5624	1412	2602	95	below_threshold
Paraburkholderia bannensis	strain=NBRC 103871	GCA_000685015.1	765414	765414	type	True	84.2417	1414	2602	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.4928	1110	2602	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.4882	1067	2602	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.2889	1140	2602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,961] [INFO] DFAST Taxonomy check result was written to GCF_000685035.1_ASM68503v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:09,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:09,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:09,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/checkm_data
[2024-01-24 13:47:09,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:10,038] [INFO] Task started: CheckM
[2024-01-24 13:47:10,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685035.1_ASM68503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685035.1_ASM68503v1_genomic.fna/checkm_input GCF_000685035.1_ASM68503v1_genomic.fna/checkm_result
[2024-01-24 13:48:15,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:15,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:15,716] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:15,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:15,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685035.1_ASM68503v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:15,717] [INFO] Task started: Blastn
[2024-01-24 13:48:15,717] [INFO] Running command: blastn -query GCF_000685035.1_ASM68503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de934dc-9c69-4d22-826f-074b6f01d497/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685035.1_ASM68503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:17,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:17,740] [INFO] Selected 16 target genomes.
[2024-01-24 13:48:17,741] [INFO] Target genome list was writen to GCF_000685035.1_ASM68503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:17,754] [INFO] Task started: fastANI
[2024-01-24 13:48:17,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac3548f-53e8-4a0c-a6ab-af36fef832f3/GCF_000685035.1_ASM68503v1_genomic.fna.gz --refList GCF_000685035.1_ASM68503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000685035.1_ASM68503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:46,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:46,615] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:46,615] [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_000685035.1	s__Paraburkholderia ferrariae	100.0	2597	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000684975.1	s__Paraburkholderia acidipaludis	87.3372	1444	2602	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	85.1434	1380	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519185.1	s__Paraburkholderia nodosa	85.0837	1454	2602	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	85.034	1410	2602	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	85.0273	1409	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_003268775.1	s__Paraburkholderia unamae	85.0078	1512	2602	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	85.0034	1450	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	84.9908	1424	2602	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	84.9157	1401	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353915.1	s__Paraburkholderia sp004353915	84.8931	1397	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785435.2	s__Paraburkholderia sacchari	84.8005	1292	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_003837865.1	s__Paraburkholderia dinghuensis	84.7737	1150	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789675.1	s__Paraburkholderia acidisoli	84.6262	1402	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848665.1	s__Paraburkholderia hiiakae	84.5702	1411	2602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685015.1	s__Paraburkholderia bannensis	84.2411	1414	2602	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 13:48:46,617] [INFO] GTDB search result was written to GCF_000685035.1_ASM68503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:46,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:46,622] [INFO] DFAST_QC result json was written to GCF_000685035.1_ASM68503v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:46,622] [INFO] DFAST_QC completed!
[2024-01-24 13:48:46,622] [INFO] Total running time: 0h2m43s