[2024-01-24 13:17:14,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference
[2024-01-24 13:17:15,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,894] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg59071e30-e916-40b9-838b-0f326fad7a45/GCF_000767615.3_ASM76761v3_genomic.fna.gz | prodigal -d GCF_000767615.3_ASM76761v3_genomic.fna/cds.fna -a GCF_000767615.3_ASM76761v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:35,714] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:35,714] [INFO] Task started: HMMsearch
[2024-01-24 13:17:35,714] [INFO] Running command: hmmsearch --tblout GCF_000767615.3_ASM76761v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/reference_markers.hmm GCF_000767615.3_ASM76761v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:36,054] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:36,056] [INFO] Found 6/6 markers.
[2024-01-24 13:17:36,103] [INFO] Query marker FASTA was written to GCF_000767615.3_ASM76761v3_genomic.fna/markers.fasta
[2024-01-24 13:17:36,103] [INFO] Task started: Blastn
[2024-01-24 13:17:36,104] [INFO] Running command: blastn -query GCF_000767615.3_ASM76761v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/reference_markers.fasta -out GCF_000767615.3_ASM76761v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:37,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:37,038] [INFO] Selected 22 target genomes.
[2024-01-24 13:17:37,039] [INFO] Target genome list was writen to GCF_000767615.3_ASM76761v3_genomic.fna/target_genomes.txt
[2024-01-24 13:17:37,044] [INFO] Task started: fastANI
[2024-01-24 13:17:37,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg59071e30-e916-40b9-838b-0f326fad7a45/GCF_000767615.3_ASM76761v3_genomic.fna.gz --refList GCF_000767615.3_ASM76761v3_genomic.fna/target_genomes.txt --output GCF_000767615.3_ASM76761v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:02,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:02,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,898] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:02,899] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:02,899] [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=DSM 16536	GCA_000767615.3	93220	93220	type	True	100.0	1796	1796	95	inconclusive
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	99.9977	1796	1796	95	inconclusive
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	95.1142	1598	1796	95	inconclusive
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	85.2132	1318	1796	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	85.1748	1249	1796	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	85.1601	1288	1796	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	85.1409	1319	1796	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	84.8722	1288	1796	95	below_threshold
Pandoraea capi	strain=LMG 20602	GCA_902459735.1	2508286	2508286	type	True	84.8695	1337	1796	95	below_threshold
Pandoraea cepalis	strain=LMG 31106	GCA_902459665.1	2508294	2508294	type	True	84.7939	1237	1796	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	84.688	1298	1796	95	below_threshold
Pandoraea anhela	strain=LMG 31108	GCA_902459655.1	2508295	2508295	type	True	84.5542	1273	1796	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	84.4269	1332	1796	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.6633	637	1796	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3648	508	1796	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	78.29	470	1796	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.1398	460	1796	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	78.0295	388	1796	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	77.0794	197	1796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,901] [INFO] DFAST Taxonomy check result was written to GCF_000767615.3_ASM76761v3_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/checkm_data
[2024-01-24 13:18:02,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,978] [INFO] Task started: CheckM
[2024-01-24 13:18:02,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000767615.3_ASM76761v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000767615.3_ASM76761v3_genomic.fna/checkm_input GCF_000767615.3_ASM76761v3_genomic.fna/checkm_result
[2024-01-24 13:19:15,943] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:15,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:15,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:15,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000767615.3_ASM76761v3_genomic.fna/markers.fasta)
[2024-01-24 13:19:15,970] [INFO] Task started: Blastn
[2024-01-24 13:19:15,970] [INFO] Running command: blastn -query GCF_000767615.3_ASM76761v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9cd02ca-fb79-4dc9-b307-f18039402f91/dqc_reference/reference_markers_gtdb.fasta -out GCF_000767615.3_ASM76761v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,803] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:17,803] [INFO] Target genome list was writen to GCF_000767615.3_ASM76761v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:17,821] [INFO] Task started: fastANI
[2024-01-24 13:19:17,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg59071e30-e916-40b9-838b-0f326fad7a45/GCF_000767615.3_ASM76761v3_genomic.fna.gz --refList GCF_000767615.3_ASM76761v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000767615.3_ASM76761v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:44,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:44,344] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:44,345] [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	100.0	1796	1796	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_902459725.1	s__Pandoraea eparura	85.1851	1218	1796	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	85.1648	1250	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
GCF_902459805.1	s__Pandoraea bronchicola	85.1638	1288	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000815105.2	s__Pandoraea pulmonicola	85.1327	1318	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459565.1	s__Pandoraea aquatica	84.9588	1330	1796	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	84.8849	1335	1796	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	84.8502	1291	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459665.1	s__Pandoraea cepalis	84.8088	1235	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	97.00	95.81	0.88	0.85	6	-
GCF_902459615.1	s__Pandoraea commovens	84.6999	1339	1796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459555.1	s__Pandoraea horticolens	84.6956	1297	1796	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	84.6627	1337	1796	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	84.5718	1271	1796	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	84.5251	1318	1796	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	84.4288	1333	1796	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	83.8173	1277	1796	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	77.0269	225	1796	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	76.3047	130	1796	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	75.2774	85	1796	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 13:19:44,346] [INFO] GTDB search result was written to GCF_000767615.3_ASM76761v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:44,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:44,351] [INFO] DFAST_QC result json was written to GCF_000767615.3_ASM76761v3_genomic.fna/dqc_result.json
[2024-01-24 13:19:44,351] [INFO] DFAST_QC completed!
[2024-01-24 13:19:44,351] [INFO] Total running time: 0h2m30s