[2024-01-24 13:55:48,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:48,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:48,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference
[2024-01-24 13:55:49,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,583] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,583] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8e1ebd8-6c1b-4c3b-9915-bbea9aff81b7/GCF_000684975.1_ASM68497v1_genomic.fna.gz | prodigal -d GCF_000684975.1_ASM68497v1_genomic.fna/cds.fna -a GCF_000684975.1_ASM68497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:08,941] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:08,941] [INFO] Task started: HMMsearch
[2024-01-24 13:56:08,942] [INFO] Running command: hmmsearch --tblout GCF_000684975.1_ASM68497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/reference_markers.hmm GCF_000684975.1_ASM68497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:09,325] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:09,328] [INFO] Found 6/6 markers.
[2024-01-24 13:56:09,381] [INFO] Query marker FASTA was written to GCF_000684975.1_ASM68497v1_genomic.fna/markers.fasta
[2024-01-24 13:56:09,382] [INFO] Task started: Blastn
[2024-01-24 13:56:09,382] [INFO] Running command: blastn -query GCF_000684975.1_ASM68497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/reference_markers.fasta -out GCF_000684975.1_ASM68497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:10,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:10,422] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:10,423] [INFO] Target genome list was writen to GCF_000684975.1_ASM68497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:10,440] [INFO] Task started: fastANI
[2024-01-24 13:56:10,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e1ebd8-6c1b-4c3b-9915-bbea9aff81b7/GCF_000684975.1_ASM68497v1_genomic.fna.gz --refList GCF_000684975.1_ASM68497v1_genomic.fna/target_genomes.txt --output GCF_000684975.1_ASM68497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:44,606] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:44,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:44,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:44,627] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:44,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:44,627] [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 acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	100.0	2128	2130	95	conclusive
Paraburkholderia ferrariae	strain=NBRC 106233	GCA_000685035.1	386056	386056	type	True	87.4513	1440	2130	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	85.1188	1392	2130	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	85.0353	1374	2130	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	84.9448	1372	2130	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	84.9268	1291	2130	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	84.8493	1374	2130	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	84.8012	1430	2130	95	below_threshold
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	84.7878	1257	2130	95	below_threshold
Paraburkholderia acidiphila	strain=7Q-K02	GCA_009789655.1	2571747	2571747	type	True	84.7827	1405	2130	95	below_threshold
Paraburkholderia dinghuensis	strain=DHOA04	GCA_003837865.1	2305225	2305225	type	True	84.7658	1153	2130	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_902833725.1	312026	312026	type	True	84.7557	1270	2130	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_000472825.1	312026	312026	type	True	84.7286	1258	2130	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_900109265.1	92647	92647	type	True	84.7091	1385	2130	95	below_threshold
Paraburkholderia tropica	strain=Ppe8	GCA_002071575.1	92647	92647	type	True	84.6983	1385	2130	95	below_threshold
Paraburkholderia tropica	strain=LMG 22274	GCA_902833865.1	92647	92647	type	True	84.6539	1399	2130	95	below_threshold
Paraburkholderia eburnea	strain=JCM 18070	GCA_002917095.1	1189126	1189126	type	True	84.3659	1339	2130	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.7258	1018	2130	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.6297	1046	2130	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.3326	1124	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:44,629] [INFO] DFAST Taxonomy check result was written to GCF_000684975.1_ASM68497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:44,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:44,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:44,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/checkm_data
[2024-01-24 13:56:44,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:44,697] [INFO] Task started: CheckM
[2024-01-24 13:56:44,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000684975.1_ASM68497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000684975.1_ASM68497v1_genomic.fna/checkm_input GCF_000684975.1_ASM68497v1_genomic.fna/checkm_result
[2024-01-24 13:57:40,086] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:40,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:40,103] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:40,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:40,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000684975.1_ASM68497v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:40,104] [INFO] Task started: Blastn
[2024-01-24 13:57:40,104] [INFO] Running command: blastn -query GCF_000684975.1_ASM68497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e94e414-cdd0-45eb-ba94-c06c5ae25875/dqc_reference/reference_markers_gtdb.fasta -out GCF_000684975.1_ASM68497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:42,041] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:42,046] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:42,046] [INFO] Target genome list was writen to GCF_000684975.1_ASM68497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:42,110] [INFO] Task started: fastANI
[2024-01-24 13:57:42,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e1ebd8-6c1b-4c3b-9915-bbea9aff81b7/GCF_000684975.1_ASM68497v1_genomic.fna.gz --refList GCF_000684975.1_ASM68497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000684975.1_ASM68497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:10,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:10,014] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:10,014] [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_000684975.1	s__Paraburkholderia acidipaludis	100.0	2128	2130	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_000685035.1	s__Paraburkholderia ferrariae	87.4425	1441	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298475.1	s__Paraburkholderia sp004298475	85.4104	1020	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.94	99.94	0.88	0.88	2	-
GCF_003268775.1	s__Paraburkholderia unamae	85.0325	1396	2130	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	85.0164	1377	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	85.0033	1336	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	84.969	1372	2130	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	84.9202	1292	2130	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	84.868	1448	2130	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	84.8628	1372	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	N/A	N/A	N/A	N/A	1	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	84.8333	1426	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739815.1	s__Paraburkholderia mimosarum	84.7987	1255	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.63	98.93	0.95	0.86	4	-
GCF_009789655.1	s__Paraburkholderia acidiphila	84.7964	1403	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837865.1	s__Paraburkholderia dinghuensis	84.7494	1155	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109265.1	s__Paraburkholderia tropica	84.6746	1391	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.07	95.97	0.93	0.85	14	-
GCF_009789675.1	s__Paraburkholderia acidisoli	84.2869	1347	2130	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 13:58:10,016] [INFO] GTDB search result was written to GCF_000684975.1_ASM68497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:10,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:10,026] [INFO] DFAST_QC result json was written to GCF_000684975.1_ASM68497v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:10,026] [INFO] DFAST_QC completed!
[2024-01-24 13:58:10,026] [INFO] Total running time: 0h2m22s