[2024-01-24 10:47:08,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,908] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg7820b6e8-9e34-48e5-b5dc-bc697bc56b71/GCF_900454355.1_52184_F01_genomic.fna.gz | prodigal -d GCF_900454355.1_52184_F01_genomic.fna/cds.fna -a GCF_900454355.1_52184_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:30,329] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:30,329] [INFO] Task started: HMMsearch
[2024-01-24 10:47:30,329] [INFO] Running command: hmmsearch --tblout GCF_900454355.1_52184_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/reference_markers.hmm GCF_900454355.1_52184_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:30,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:30,649] [INFO] Found 6/6 markers.
[2024-01-24 10:47:30,691] [INFO] Query marker FASTA was written to GCF_900454355.1_52184_F01_genomic.fna/markers.fasta
[2024-01-24 10:47:30,692] [INFO] Task started: Blastn
[2024-01-24 10:47:30,692] [INFO] Running command: blastn -query GCF_900454355.1_52184_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/reference_markers.fasta -out GCF_900454355.1_52184_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:31,601] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:31,604] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:31,605] [INFO] Target genome list was writen to GCF_900454355.1_52184_F01_genomic.fna/target_genomes.txt
[2024-01-24 10:47:31,869] [INFO] Task started: fastANI
[2024-01-24 10:47:31,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg7820b6e8-9e34-48e5-b5dc-bc697bc56b71/GCF_900454355.1_52184_F01_genomic.fna.gz --refList GCF_900454355.1_52184_F01_genomic.fna/target_genomes.txt --output GCF_900454355.1_52184_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,812] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,828] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:58,828] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:58,829] [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 pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	100.0	1817	1823	95	inconclusive
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	99.9963	1796	1823	95	inconclusive
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	95.1375	1598	1823	95	inconclusive
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	85.1629	1256	1823	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	85.1518	1294	1823	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	85.1377	1306	1823	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	85.1085	1290	1823	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.8981	1328	1823	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	84.8069	1302	1823	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	84.7454	1223	1823	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	84.6656	1295	1823	95	below_threshold
Pandoraea anhela	strain=LMG 31108	GCA_902459655.1	2508295	2508295	type	True	84.5836	1259	1823	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	84.479	1331	1823	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.7903	647	1823	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.39	460	1823	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3287	531	1823	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.1689	456	1823	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.0291	382	1823	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	77.2624	195	1823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,831] [INFO] DFAST Taxonomy check result was written to GCF_900454355.1_52184_F01_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,831] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/checkm_data
[2024-01-24 10:47:58,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,888] [INFO] Task started: CheckM
[2024-01-24 10:47:58,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454355.1_52184_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454355.1_52184_F01_genomic.fna/checkm_input GCF_900454355.1_52184_F01_genomic.fna/checkm_result
[2024-01-24 10:49:04,894] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:04,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:04,921] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:04,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:04,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454355.1_52184_F01_genomic.fna/markers.fasta)
[2024-01-24 10:49:04,922] [INFO] Task started: Blastn
[2024-01-24 10:49:04,922] [INFO] Running command: blastn -query GCF_900454355.1_52184_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a6846f6-ddbd-415f-a694-c501ae2d6ece/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454355.1_52184_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:06,457] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:06,460] [INFO] Selected 20 target genomes.
[2024-01-24 10:49:06,460] [INFO] Target genome list was writen to GCF_900454355.1_52184_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:06,480] [INFO] Task started: fastANI
[2024-01-24 10:49:06,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg7820b6e8-9e34-48e5-b5dc-bc697bc56b71/GCF_900454355.1_52184_F01_genomic.fna.gz --refList GCF_900454355.1_52184_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454355.1_52184_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:30,160] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:30,178] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:30,178] [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	99.9963	1795	1823	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_902459585.1	s__Pandoraea nosoerga	85.1553	1257	1823	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	85.1467	1294	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459805.1	s__Pandoraea bronchicola	85.1085	1290	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459725.1	s__Pandoraea eparura	85.0665	1222	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459565.1	s__Pandoraea aquatica	84.934	1352	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459735.1	s__Pandoraea capi	84.8823	1330	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	96.45	96.45	0.90	0.90	2	-
GCF_902459745.1	s__Pandoraea communis	84.7964	1304	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459615.1	s__Pandoraea commovens	84.7445	1355	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459665.1	s__Pandoraea cepalis	84.7392	1224	1823	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	84.6656	1295	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_000814845.2	s__Pandoraea sputorum	84.6152	1350	1823	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	84.5928	1258	1823	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	84.5088	1330	1823	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	84.4659	1333	1823	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	83.7544	1283	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_004216565.1	s__Leptothrix mobilis	77.1046	224	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903975.1	s__UBA4615 sp903903975	76.2781	116	1823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	99.67	99.60	0.92	0.90	5	-
GCA_016713435.1	s__JADJOM01 sp016713435	75.1254	94	1823	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:30,180] [INFO] GTDB search result was written to GCF_900454355.1_52184_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:30,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:30,184] [INFO] DFAST_QC result json was written to GCF_900454355.1_52184_F01_genomic.fna/dqc_result.json
[2024-01-24 10:49:30,185] [INFO] DFAST_QC completed!
[2024-01-24 10:49:30,185] [INFO] Total running time: 0h2m21s