[2024-01-24 13:48:58,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:58,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:58,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference
[2024-01-24 13:49:00,092] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,094] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg58d0be60-91da-47ab-99e9-06f7f8344e37/GCF_902459575.1_LMG_31116_genomic.fna.gz | prodigal -d GCF_902459575.1_LMG_31116_genomic.fna/cds.fna -a GCF_902459575.1_LMG_31116_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:17,365] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:17,365] [INFO] Task started: HMMsearch
[2024-01-24 13:49:17,366] [INFO] Running command: hmmsearch --tblout GCF_902459575.1_LMG_31116_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/reference_markers.hmm GCF_902459575.1_LMG_31116_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:17,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:17,685] [INFO] Found 6/6 markers.
[2024-01-24 13:49:17,728] [INFO] Query marker FASTA was written to GCF_902459575.1_LMG_31116_genomic.fna/markers.fasta
[2024-01-24 13:49:17,728] [INFO] Task started: Blastn
[2024-01-24 13:49:17,728] [INFO] Running command: blastn -query GCF_902459575.1_LMG_31116_genomic.fna/markers.fasta -db /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/reference_markers.fasta -out GCF_902459575.1_LMG_31116_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:18,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:18,757] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:18,758] [INFO] Target genome list was writen to GCF_902459575.1_LMG_31116_genomic.fna/target_genomes.txt
[2024-01-24 13:49:18,765] [INFO] Task started: fastANI
[2024-01-24 13:49:18,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d0be60-91da-47ab-99e9-06f7f8344e37/GCF_902459575.1_LMG_31116_genomic.fna.gz --refList GCF_902459575.1_LMG_31116_genomic.fna/target_genomes.txt --output GCF_902459575.1_LMG_31116_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:41,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:41,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:41,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:41,096] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:41,097] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:41,097] [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
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	100.0	1725	1725	95	inconclusive
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	95.1165	1594	1725	95	inconclusive
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	95.1025	1612	1725	95	inconclusive
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	85.0344	1270	1725	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	85.022	1232	1725	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	84.9899	1289	1725	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	84.9395	1294	1725	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	84.706	1223	1725	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	84.5831	1250	1725	95	below_threshold
Pandoraea oxalativorans	strain=DSM 23570	GCA_000972785.3	573737	573737	type	True	84.4559	1289	1725	95	below_threshold
Pandoraea vervacti	strain=NS15	GCA_000934605.2	656178	656178	type	True	84.3381	1290	1725	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	84.3056	1290	1725	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	78.4579	582	1725	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3426	520	1725	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.2851	524	1725	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.0097	373	1725	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	77.9276	452	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,099] [INFO] DFAST Taxonomy check result was written to GCF_902459575.1_LMG_31116_genomic.fna/tc_result.tsv
[2024-01-24 13:49:41,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:41,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:41,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/checkm_data
[2024-01-24 13:49:41,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:41,151] [INFO] Task started: CheckM
[2024-01-24 13:49:41,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902459575.1_LMG_31116_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902459575.1_LMG_31116_genomic.fna/checkm_input GCF_902459575.1_LMG_31116_genomic.fna/checkm_result
[2024-01-24 13:50:36,748] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:36,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,774] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:36,774] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:36,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902459575.1_LMG_31116_genomic.fna/markers.fasta)
[2024-01-24 13:50:36,775] [INFO] Task started: Blastn
[2024-01-24 13:50:36,775] [INFO] Running command: blastn -query GCF_902459575.1_LMG_31116_genomic.fna/markers.fasta -db /var/lib/cwl/stg90285709-951b-4d54-b4f9-efac02c93a10/dqc_reference/reference_markers_gtdb.fasta -out GCF_902459575.1_LMG_31116_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,776] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:38,776] [INFO] Target genome list was writen to GCF_902459575.1_LMG_31116_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:38,828] [INFO] Task started: fastANI
[2024-01-24 13:50:38,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d0be60-91da-47ab-99e9-06f7f8344e37/GCF_902459575.1_LMG_31116_genomic.fna.gz --refList GCF_902459575.1_LMG_31116_genomic.fna/target_genomes_gtdb.txt --output GCF_902459575.1_LMG_31116_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:02,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:02,860] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:02,860] [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_000767615.3	s__Pandoraea pnomenusa	95.1165	1594	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	conclusive
GCF_902459805.1	s__Pandoraea bronchicola	85.0365	1270	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459585.1	s__Pandoraea nosoerga	85.0041	1235	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
GCF_000815105.2	s__Pandoraea pulmonicola	84.9457	1293	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459725.1	s__Pandoraea eparura	84.8862	1226	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	84.7879	1267	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_000807775.2	s__Pandoraea fibrosis	84.7715	1292	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	-
GCF_902459735.1	s__Pandoraea capi	84.71	1318	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_902459665.1	s__Pandoraea cepalis	84.6979	1224	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	-
GCF_902459555.1	s__Pandoraea horticolens	84.575	1251	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_000972785.3	s__Pandoraea oxalativorans	84.4516	1290	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814845.2	s__Pandoraea sputorum	84.4298	1333	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.03	97.40	0.96	0.92	5	-
GCF_902459655.1	s__Pandoraea anhela	84.367	1254	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459765.1	s__Pandoraea anapnoica	84.3607	1357	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029105.3	s__Pandoraea faecigallinarum	84.3456	1280	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934605.2	s__Pandoraea vervacti	84.3375	1290	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459775.1	s__Pandoraea captiosa	84.2918	1292	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179965.1	s__Pandoraea sp002179965	83.7036	1242	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_001465545.3	s__Pandoraea norimbergensis	83.5975	1272	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:02,862] [INFO] GTDB search result was written to GCF_902459575.1_LMG_31116_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:02,862] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:02,866] [INFO] DFAST_QC result json was written to GCF_902459575.1_LMG_31116_genomic.fna/dqc_result.json
[2024-01-24 13:51:02,866] [INFO] DFAST_QC completed!
[2024-01-24 13:51:02,867] [INFO] Total running time: 0h2m4s